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1.  Urinary phthalate metabolites in relation to maternal serum thyroid and sex hormone levels during pregnancy: a longitudinal analysis 
Increasing scientific evidence suggests that exposure to phthalates during pregnancy may be associated with an elevated risk of adverse reproductive outcomes such as preterm birth. Maternal endocrine disruption across pregnancy may be one pathway mediating some of these relationships. We investigated whether urinary phthalate metabolites were associated with maternal serum thyroid (free thyroxine [FT4], free triiodothyronine [FT3], and thyroid-stimulating hormone [TSH]), and sex (estradiol, progesterone, and sex hormone-binding globulin [SHBG]) hormone levels at multiple time points during pregnancy.
Preliminary data (n = 106) were obtained from an ongoing prospective birth cohort in Northern Puerto Rico. We collected urine and serum sample at the first and third study visits that occurred at 18 +/- 2 and 26 +/- 2 weeks of gestation, respectively. To explore the longitudinal relationships between urinary phthalate metabolites and serum thyroid and sex hormone concentrations, we used linear mixed models (LMMs) adjusted for prepregnancy body mass index (BMI) and maternal age. An interaction term was added to each LMM to test whether the effect of urinary phthalate metabolites on serum thyroid and sex hormone levels varied by study visit. In cross-sectional analyses, we stratified BMI- and age-adjusted linear regression models by study visit.
In adjusted LMMs, we observed significant inverse associations between mono-3-carboxypropyl phthalate (MCPP) and FT3 and between mono-ethyl phthalate (MEP) and progesterone. In cross-sectional analyses by study visit, we detected stronger and statistically significant inverse associations at the third study visit between FT3 and MCPP as well as mono-carboxyisooctyl phthalate (MCOP); also at the third study visit, significant inverse associations were observed between FT4 and metabolites of di-(2-ethylhexyl) phthalate (DEHP). The inverse association between MEP and progesterone was consistent across study visits.
In this group of pregnant women, urinary phthalate metabolites may be associated with altered maternal serum thyroid and sex hormone levels, and the magnitude of these effects may depend on the timing of exposure during gestation.
Electronic supplementary material
The online version of this article (doi:10.1186/1477-7827-13-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4326411  PMID: 25596636
Biomarkers; Endocrine disruption; Epidemiology; Thyroid; Hormones; Urinary metabolites; Pregnancy; Phthalates
2.  Urinary phthalate metabolite concentrations among pregnant women in Northern Puerto Rico: Distribution, temporal variability, and predictors 
Environment international  2013;62:10.1016/j.envint.2013.09.014.
Phthalate contamination exists in the North coast karst aquifer system in Puerto Rico. In light of potential health impacts associated with phthalate exposure, targeted action for elimination of exposure sources may be warranted, especially for sensitive populations such as pregnant women. However, information on exposure to phthalates from a variety of sources in Puerto Rico is lacking. The objective of this study was to determine concentrations and predictors of urinary phthalate biomarkers measured at multiple times during pregnancy among women living in the Northern karst area of Puerto Rico.
We recruited 139 pregnant women in Northern Puerto Rico and collected urine samples and questionnaire data at three separate visits (18±2 weeks, 22±2 weeks, and 26±2 weeks of gestation). Urine samples were analyzed for eleven phthalate metabolites: mono-2-ethylhexyl phthalate (MEHP), mono-2-ethyl-5-hydroxyhexyl phthalate, mono-2-ethyl-5-oxohexyl phthalate, mono-2-ethyl-5-carboxypentyl phthalate, mono-ethyl phthalate (MEP), mono-n-butyl phthalate, mono-benzyl phthalate, mono-isobutyl phthalate, mono-3-carboxypropyl phthalate (MCPP), mono carboxyisononyl phthalate (MCNP), and mono carboxyisooctyl phthalate (MCOP).
Detectable concentrations of phthalate metabolites among pregnant women living in Puerto Rico was prevalent, and metabolite concentrations tended to be higher than or similar to those measured in women of reproductive age from the general US population. Intraclass correlation coefficients ranged from very weak (MCNP; 0.05) to moderate (MEP; 0.44) reproducibility among all phthalate metabolites. We observed significant or suggestive positive associations between urinary phthalate metabolites concentrations and water usage/storage habits (MEP, MCNP, MCOP), use of personal care products (MEP), and consumption of certain food items (MCPP, MCNP, and MCOP).
To our knowledge this is the first study to report concentrations, temporal variability, and predictors of phthalate biomarkers among pregnant women in Puerto Rico. Preliminary results suggest several potentially important exposure sources to phthalates in this population and future analysis from this ongoing prospective cohort will help to inform targeted approaches to reduce exposure.
PMCID: PMC3874859  PMID: 24161445
biomarker; endocrine disruptor; phthalates; environment; epidemiology; exposure; pregnancy
3.  Plasma Levels of Dimethylarginines in Preterm Very Low Birth Weight Neonates: Its Relation with Perinatal Factors and Short-Term Outcome 
Endogenously produced inhibitors of nitric oxide (NO) synthase, in particular asymmetric dimethylarginine (ADMA), are currently considered of importance in various disease states characterized by reduced NO availability. We investigated the association between plasma levels of ADMA, symmetric dimethylarginine (SDMA), l-arginine, and citrulline and perinatal factors and outcome in 130 preterm (gestational age ≤30 weeks) very low birth weight (VLBW, <1500 g) infants. Plasma samples were collected 6–12 h after birth. We did not find significant correlations between ADMA, SDMA, l-arginine, and citrulline levels and gestational age or birth weight. However, the arginine:ADMA ratio (AAR, a better indicator of NO availability than either arginine or ADMA separately) was positively correlated with gestational age. ADMA and arginine levels were not significantly different between males and females but males showed a negative correlation between ADMA levels and gestational age. Perinatal factors such as preeclampsia, chrorioamnionitis, prolonged rupture of membranes, or form of delivery did not significantly alter dimethylarginine levels or AAR. In contrast, the AAR was significantly reduced in the infants with respiratory distress, mechanical ventilation, and systemic hypotension Therefore, our data suggest that altered NO availability may play a role in the respiratory and cardiovascular adaptation in preterm VLBW infants.
PMCID: PMC4307233  PMID: 25546385
dimethylarginine; arginine; preterm infants; nitric oxide; preeclampsia; chrorioamnionitis; respiratory distress
4.  High-Quality Draft Genome Sequence of Babesia divergens, the Etiological Agent of Cattle and Human Babesiosis 
Genome Announcements  2014;2(6):e01194-14.
Babesia divergens causes significant morbidity and mortality in cattle and splenectomized or immunocompromised individuals. Here, we present a 10.7-Mb high-quality draft genome of this parasite close to chromosome resolution that will enable comparative genome analyses and synteny studies among related parasites.
PMCID: PMC4241675  PMID: 25395649
5.  Invasive maxillary sinus aspergillosis: A case report successfully treated with voriconazole and surgical debridement 
Introduction: Invasive aspergillosis of the paranasal sinuses is a rare disease and often misdiagnosed; however, its incidence has seen substancial growth over the past 2 decades. Definitive diagnosis of these lesions is based on histological examination and fungal culture. Case Report: An 81-year-old woman with a history of pain in the left maxillary region is presented. The diagnosis was invasive maxillary aspergillosis in immunocompetent patient, which was successfully treated with voriconazole and surgical debridement. Possible clinical manifestations, diagnostic imaging techniques and treatment used are discussed. Since the introduction of voriconazole, there have been several reports of patients with invasive aspergillosis who responded to treatment with this new antifungal agent. Conclusions: We report the importance of early diagnosis and selection of an appropriate antifungal agent to achieve a successful treatment.
Key words:Invasive aspergillosis, voriconazole, fungal sinusitis, antifungal agent, open sinus surgery.
PMCID: PMC4282918  PMID: 25593673
6.  Radiobiological comparison of two radiotherapy treatment techniques for high-risk prostate cancer 
To make a radiobiological comparison, for high risk prostate cancer (T3a, PSA > 20 ng/ml or Gleason > 7) of two radiotherapy treatment techniques. One technique consists of a treatment in three phases of the pelvic nodes, vesicles and prostate using a conventional fractionation scheme of 2 Gy/fraction (SIMRT). The other technique consists of a treatment in two phases that gives simultaneously different dose levels in each phase, 2 Gy/fraction, 2.25 Gy/fraction and 2.5 Gy/fraction to the pelvic nodes, vesicles and prostate, respectively (SIBIMRT).
Materials and methods
The equivalent dose at fractionation of 2 Gy (EQD2), calculated using the linear quadratic model with α/βprostate = 1.5 Gy, was the same for both treatment strategies. For comparison the parameters employed were D95, mean dose and Tumour Control Probabilities for prostate PTV and D15, D25, D35, D50, mean dose and Normal Tissue Complication Probabilities for the rectum and bladder, with physical doses converted to EQD2. Parameters were obtained for α/βprostate = 1.5, 3 and 10 Gy and for α/βoar = 1, 2, 3, 4, 6 and 8.
For prostate PTV, both treatment strategies are equivalent for α/βprostate = 1.5 Gy but for higher α/βprostate, EQD2 and TCP, decrease for the SIBIMRT technique. For the rectum and bladder when α/βoar ≤ 2 Gy, EQD2 and NTCP are lower for the SIMRT technique or equal in both techniques. For α/βoar ≥ 2–3 Gy, EQD2 and NTCP increase for the SIMRT treatment.
A comparison between two radiotherapy techniques is presented. The SIBIMRT technique reduces EQD2 and NTCP for α/βoar from 2 to 8 Gy.
PMCID: PMC3863222  PMID: 24416563
Radiobiology; Simultaneous integrated boost; NTCP; Equivalent dose at fractionation of 2 Gy (EQD2); Prostate
7.  Dedifferentiated Giant-Cell Tumor of Bone with an Undifferentiated Round Cell Mesenchymal Component 
Rare Tumors  2014;6(3):5319.
The dedifferentiated giant-cell tumor of the bone is a very rare variant of the giant-cell tumor (GCT). We report the clinical, radiographic and histological findings of a dedifferentiated GCT in which the dedifferentiated component consisted of small round cells. We also comment on previously reported cases of dedifferentiated GCT, discuss the clinical implications of this dual histology, and analyze the information published about the coexistence of similar genetic abnormalities in GCT and small round cell tumors of the bone.
PMCID: PMC4178272  PMID: 25276319
dedifferentiated; giant-cell tumor; bone tumor
8.  Respiratory Mechanics and Plasma Levels of Tumor Necrosis Factor Alpha and Interleukin 6 Are Affected by Gas Humidification during Mechanical Ventilation in Dogs 
PLoS ONE  2014;9(7):e101952.
The use of dry gases during mechanical ventilation has been associated with the risk of serious airway complications. The goal of the present study was to quantify the plasma levels of TNF-alpha and IL-6 and to determine the radiological, hemodynamic, gasometric, and microscopic changes in lung mechanics in dogs subjected to short-term mechanical ventilation with and without humidification of the inhaled gas. The experiment was conducted for 24 hours in 10 dogs divided into two groups: Group I (n = 5), mechanical ventilation with dry oxygen dispensation, and Group II (n = 5), mechanical ventilation with oxygen dispensation using a moisture chamber. Variance analysis was used. No changes in physiological, hemodynamic, or gasometric, and radiographic constants were observed. Plasma TNF-alpha levels increased in group I, reaching a maximum 24 hours after mechanical ventilation was initiated (ANOVA p = 0.77). This increase was correlated to changes in mechanical ventilation. Plasma IL-6 levels decreased at 12 hours and increased again towards the end of the study (ANOVA p>0.05). Both groups exhibited a decrease in lung compliance and functional residual capacity values, but this was more pronounced in group I. Pplat increased in group I (ANOVA p = 0.02). Inhalation of dry gas caused histological lesions in the entire respiratory tract, including pulmonary parenchyma, to a greater extent than humidified gas. Humidification of inspired gases can attenuate damage associated with mechanical ventilation.
PMCID: PMC4103761  PMID: 25036811
9.  Zoonotic Filariasis Caused by Novel Brugia sp. Nematode, United States, 2011 
Emerging Infectious Diseases  2014;20(7):1248-1250.
PMCID: PMC4073870  PMID: 24963722
Brugia sp. Nov; zoonotic filariasis; North America; New York; United States; parasites; nematode
10.  Screen Media Usage, Sleep Time and Academic Performance in Adolescents: Clustering a Self-Organizing Maps Analysis 
PLoS ONE  2014;9(6):e99478.
Screen media usage, sleep time and socio-demographic features are related to adolescents' academic performance, but interrelations are little explored. This paper describes these interrelations and behavioral profiles clustered in low and high academic performance. A nationally representative sample of 3,095 Spanish adolescents, aged 12 to 18, was surveyed on 15 variables linked to the purpose of the study. A Self-Organizing Maps analysis established non-linear interrelationships among these variables and identified behavior patterns in subsequent cluster analyses. Topological interrelationships established from the 15 emerging maps indicated that boys used more passive videogames and computers for playing than girls, who tended to use mobile phones to communicate with others. Adolescents with the highest academic performance were the youngest. They slept more and spent less time using sedentary screen media when compared to those with the lowest performance, and they also showed topological relationships with higher socioeconomic status adolescents. Cluster 1 grouped boys who spent more than 5.5 hours daily using sedentary screen media. Their academic performance was low and they slept an average of 8 hours daily. Cluster 2 gathered girls with an excellent academic performance, who slept nearly 9 hours per day, and devoted less time daily to sedentary screen media. Academic performance was directly related to sleep time and socioeconomic status, but inversely related to overall sedentary screen media usage. Profiles from the two clusters were strongly differentiated by gender, age, sedentary screen media usage, sleep time and academic achievement. Girls with the highest academic results had a medium socioeconomic status in Cluster 2. Findings may contribute to establishing recommendations about the timing and duration of screen media usage in adolescents and appropriate sleep time needed to successfully meet the demands of school academics and to improve interventions targeting to affect behavioral change.
PMCID: PMC4062405  PMID: 24941009
11.  Pseudomonas aeruginosa clinical and environmental isolates constitute a single population with high phenotypic diversity 
BMC Genomics  2014;15:318.
Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. In addition, genetic variability of all the P. aeruginosa strains whose genomes have been sequenced is extremely low. This low genomic variability might be explained if clinical strains constitute a subpopulation of this bacterial species present in environments that are close to human populations, which preferentially produce virulence associated traits.
In this work, we sequenced the genomes and performed phenotypic descriptions for four non-human P. aeruginosa isolates collected from a plant, the ocean, a water-spring, and from dolphin stomach. We show that the four strains are phenotypically diverse and that this is not reflected in genomic variability, since their genomes are almost identical. Furthermore, we performed a detailed comparative genomic analysis of the four strains studied in this work with the thirteen previously reported P. aeruginosa genomes by means of describing their core and pan-genomes.
Contrary to what has been described for other bacteria we have found that the P. aeruginosa core genome is constituted by a high proportion of genes and that its pan-genome is thus relatively small. Considering the high degree of genomic conservation between isolates of P. aeruginosa from diverse environments, including human tissues, some implications for the treatment of infections are discussed. This work also represents a methodological contribution for the genomic study of P. aeruginosa, since we provide a database of the comparison of all the proteins encoded by the seventeen strains analyzed.
PMCID: PMC4234422  PMID: 24773920
P. aeruginosa genomics and proteomics; Core genome; Pangenomics; Phenotypic diversity
12.  Distribution, variability and predictors of urinary concentrations of phenols and parabens among pregnant women in Puerto Rico 
Environmental science & technology  2013;47(7):3439-3447.
Puerto Rico has higher rates of a range of endocrine-related diseases and disorders compared to the United States. However, little is known to date about human exposures to known or potential endocrine disrupting chemicals (EDCs) in Puerto Rico. We recruited 105 pregnant women in Northern Puerto Rico who provided urine samples and questionnaire data at three times (20±2, 24±2, and 28±2 weeks) during gestation. We measured the urinary concentrations of five phenols and three parabens: 2,4-dichlorophenol (24-DCP), 2,5-dichlorophenol (25-DCP), benzophenone-3 (BP-3), bisphenol A (BPA), triclosan (TCS), butyl paraben (B-PB), methyl paraben (M-PB), and propyl paraben (P-PB). The frequent detection of these chemicals suggests that exposure is highly prevalent among these Puerto Rican pregnant women. Urinary concentrations of TCS, BP-3 and 25-DCP were higher than among women of reproductive age in the US general population, while concentrations of BPA, 24-DCP and parabens were similar. Intraclass correlation coefficients (ICC) varied widely between biomarkers; BPA had the lowest ICC (0.24) and BP-3 had highest (0.62), followed by 25-DCP (0.49) and TCS (0.47). We found positive associations between biomarker concentrations with self-reported use of liquid soap (TCS), sunscreen (BP-3), lotion (BP-3 and parabens), and cosmetics (parabens). Our results can inform future epidemiology studies and strategies to reduce exposure to these chemicals or their precursors.
PMCID: PMC3638245  PMID: 23469879
biomarker; endocrine disruptor; environment; epidemiology; exposure
13.  Circadian oscillatory transcriptional programs in grapevine ripening fruits 
BMC Plant Biology  2014;14:78.
Temperature and solar radiation influence Vitis vinifera L. berry ripening. Both environmental conditions fluctuate cyclically on a daily period basis and the strength of this fluctuation affects grape ripening too. Additionally, a molecular circadian clock regulates daily cyclic expression in a large proportion of the plant transcriptome modulating multiple developmental processes in diverse plant organs and developmental phases. Circadian cycling of fruit transcriptomes has not been characterized in detail despite their putative relevance in the final composition of the fruit. Thus, in this study, gene expression throughout 24 h periods in pre-ripe berries of Tempranillo and Verdejo grapevine cultivars was followed to determine whether different ripening transcriptional programs are activated during certain times of day in different grape tissues and genotypes.
Microarray analyses identified oscillatory transcriptional profiles following circadian variations in the photocycle and the thermocycle. A higher number of expression oscillating transcripts were detected in samples carrying exocarp tissue including biotic stress-responsive transcripts activated around dawn. Thermotolerance-like responses and regulation of circadian clock-related genes were observed in all studied samples. Indeed, homologs of core clock genes were identified in the grapevine genome and, among them, VvREVEILLE1 (VvRVE1), showed a consistent circadian expression rhythm in every grape berry tissue analysed. Light signalling components and terpenoid biosynthetic transcripts were specifically induced during the daytime in Verdejo, a cultivar bearing white-skinned and aromatic berries, whereas transcripts involved in phenylpropanoid biosynthesis were more prominently regulated in Tempranillo, a cultivar bearing black-skinned berries.
The transcriptome of ripening fruits varies in response to daily environmental changes, which might partially be under the control of circadian clock components. Certain cultivar and berry tissue features could rely on specific circadian oscillatory expression profiles. These findings may help to a better understanding of the progress of berry ripening in short term time scales.
PMCID: PMC3986946  PMID: 24666982
Circadian; Fruit ripening; Gene expression; Grapevine; Light; Microarray; Phenylpropanoid; Temperature; Terpene; Vitis vinifera
14.  Predictors of the Rate of Change in Disease Activity over Time in LUMINA, a Multiethnic US Cohort of Patients with Systemic Lupus Erythematosus: LUMINA LXX 
Lupus  2010;19(6):727-733.
The objectives of the present study were (1) to clarify and quantify the relationship between age and disease duration with the rate of change in disease activity over time in patients with systemic lupus erythematosus (SLE) and (2) to explore other possible factors associated with this rate of change. To this end, SLE patients from LUMINA were studied if they had ≥3 visits in which disease activity (Systemic Lupus Activity Measure-Revised or SLAM-R) had been ascertained. Variables associated with the rate (slope) of change in disease activity (obtained by regressing the SLAM-R scores against the length of time from diagnosis to last visit) were examined by univariable and multivariable analyses. Five-hundred forty-two of the 632 patients had ≥3 SLAM-R scores. In multivariable analyses Caucasians exhibited the fastest decline in disease activity; Texan Hispanics exhibited the slowest, trailed by the African Americans. Longer disease duration and HLA-DRB1*1503 positivity were associated with a slower decline whereas a greater number of ACR criteria and abnormal laboratory parameters (white blood cell and platelet counts, hematocrit and serum creatinine) were associated with a faster decline. These findings complement existing knowledge on SLE disease activity and are potentially useful to clinicians managing these patients.
PMCID: PMC3964002  PMID: 20118158
Lupus; disease activity; rate of change; ethnicity; cohort
15.  Quantitative Assessment of Mycoplasma Hemadsorption Activity by Flow Cytometry 
PLoS ONE  2014;9(1):e87500.
A number of adherent mycoplasmas have developed highly complex polar structures that are involved in diverse aspects of the biology of these microorganisms and play a key role as virulence factors by promoting adhesion to host cells in the first stages of infection. Attachment activity of mycoplasma cells has been traditionally investigated by determining their hemadsorption ability to red blood cells and it is a distinctive trait widely examined when characterizing the different mycoplasma species. Despite the fact that protocols to qualitatively determine the hemadsorption or hemagglutination of mycoplasmas are straightforward, current methods when investigating hemadsorption at the quantitative level are expensive and poorly reproducible. By using flow cytometry, we have developed a procedure to quantify rapidly and accurately the hemadsorption activity of mycoplasmas in the presence of SYBR Green I, a vital fluorochrome that stains nucleic acids, allowing to resolve erythrocyte and mycoplasma cells by their different size and fluorescence. This method is very reproducible and permits the kinetic analysis of the obtained data and a precise hemadsorption quantification based on standard binding parameters such as the dissociation constant Kd. The procedure we developed could be easily implemented in a standardized assay to test the hemadsorption activity of the growing number of clinical isolates and mutant strains of different mycoplasma species, providing valuable data about the virulence of these microorganisms.
PMCID: PMC3907496  PMID: 24498118
16.  Effect of posterior gingival smile on the perception of smile esthetics 
Objectives: To evaluate and compare the influence of posterior gummy smile on the perception of smile esthetics by orthodontists, general-dentists and laypersons. Study Design: A frontal photograph of a smile with normal gum exposure was chosen and manipulated digitally using Adobe Photoshop C3 to generate three further images with posterior gum exposure of 4, 6 and 8mm. These four images were assessed by the three evaluator groups: orthodontists (n=40), general-dentists (n=40) and laypersons (n=40). Both orthodontists and dentists had at least ten years professional experience and laypersons were aged between 40-50 years. The proportion of men to women was 20:20 in each group. Evaluators awarded a score to the smile esthetics of each image: 1=acceptable, 2=moderately acceptable, 3=unacceptable. Afterwards, each evaluator placed the four images in order of esthetic preference. Results: No significant differences (p>0.05) were detected between the three evaluator groups for the photo without posterior gummy smile. The perception of smile esthetics for a the 4mm posterior gummy smile (median for orthodontists=2, general-dentists= 1, laypersons=1), the 6mm (median for orthodontists=2, general-dentists=1, laypersons=1) and the 8mm (median for orthodontists=3, general-dentists=2, laypersons=2) was significantly different between orthodontists and the other two evaluator groups (p<0.0017). The three evaluator groups coincided in placing the image with the 6mm gum exposure in first place in order of esthetic preference. Conclusions: Posterior gummy smile influences the perception of smile esthetics more negatively among orthodontists than the rest of the groups.
Key words:Aesthetics, gummy smile back, orthodontists, dentists, laypersons.
PMCID: PMC3909438  PMID: 23986015
17.  Effectiveness of a Video-Feedback and Questioning Programme to Develop Cognitive Expertise in Sport 
PLoS ONE  2013;8(12):e82270.
The importance within sport expertise of cognitive factors has been emphasised in many research studies. Adaptations that take place in athletes’ long-term memories are going to condition their decision-making and performance, and training programmes must be developed that improve these adaptations. In our study, we provide a tactical-cognitive training programme based on video-feedback and questioning in order to improve tactical knowledge in tennis players and verify its effect when transferred to athletes’ decision-making. 11 intermediate tennis players participated in this study (12.9±0.7 years old), distributed into two groups (experimental, n = 5; control, n = 6). Tactical knowledge was measured by problem representation and strategy planning with a verbal protocol. Decision-making was measured by a systematic observation instrument. Results confirm the effectiveness of a combination of video-feedback and questioning on cognitive expertise, developing adaptations in long-term memory that produce an improvement in the quality of tactical knowledge (content, sophistication and structure). This, in turn, is transferred to the athletes’ decision-making capacity, leading to a higher percentage of successful decisions made during game play. Finally, we emphasise the need to develop effective programmes to develop cognitive expertise and improve athletes' performance, and include it in athletes’ formative stages.
PMCID: PMC3858278  PMID: 24340012
19.  Time to Neuropsychiatric Damage Occurrence in LUMINA: A Multiethnic Lupus Cohort 
Lupus  2009;18(9):822-830.
The aims of this study were to examine the predictors of time-to-neuropsychiatric (NP) damage and its impact on mortality in 632 systemic lupus erythematosus (SLE) African American, Hispanic and Caucasian LUMINA patients, age ≥ 16 years and disease duration ≤ 5 years at baseline (T0). Time-to-NP damage and its impact on mortality were examined by Cox proportional hazards regressions. One-hundred eighty-five (29.3%) patients developed NP-damage over a mean (SD) disease duration of 5.6 (3.7) years. After adjusting for neuropsychiatric manifestations present, older age [Hazard ratio (HR)=1.02; 95% [Confidence interval (CI) 1.00–1.04)], Caucasian ethnicity (HR=1.87; 95% CI 1.22-2.87), disease activity over the disease course (HR=1.16; 95% CI 1.12–1.21), diabetes (HR=3.47; 95% CI 1.44–8.38) and abnormal illness-related behaviors (HR=1.05; 95% CI 1.02–1.08) were associated with a shorter time to NP-damage. Photosensitivity (HR=0.65; 95% CI 0.44–0.95), anemia (HR=0.56; 95% CI 0.31–0.98), Raynaud’s phenomenon (HR=0.49; 95% CI 0.34–0.72), a medium dose of prednisone (HR=0.56; 95% CI 0.35–0.92) and hydroxychloroquine use (HR=0.58; 95% CI 0.36–0.93) were associated with a longer time. NP-damage did not contribute to mortality. Older age, Caucasian ethnicity, disease activity and abnormal illness-related behaviors are associated with a shorter time-to-NP damage; hydroxychloroquine and a medium dose of prednisone with a longer time.
PMCID: PMC3759150  PMID: 19578107
20.  DNA fragmentation by gamma radiation and electron beams using atomic force microscopy 
Journal of Biological Physics  2012;38(3):531-542.
Double-stranded pBS plasmid DNA was irradiated with gamma rays at doses ranging from 1 to 12 kGy and electron beams from 1 to 10 kGy. Fragment-size distributions were determined by direct visualization, using atomic force microscopy with nanometer-resolution operating in non-tapping mode, combined with an improved methodology. The fragment distributions from irradiation with gamma rays revealed discrete-like patterns at all doses, suggesting that these patterns are modulated by the base pair composition of the plasmid. Irradiation with electron beams, at very high dose rates, generated continuous distributions of highly shattered DNA fragments, similar to results at much lower dose rates found in the literature. Altogether, these results indicate that AFM could supplement traditional methods for high-resolution measurements of radiation damage to DNA, while providing new and relevant information.
PMCID: PMC3388197  PMID: 23729912
Plasmid DNA; Fragment-size distributions; AFM; Gamma radiation; Electron beams
21.  Protein Clustering and RNA Phylogenetic Reconstruction of the Influenza a Virus NS1 Protein Allow an Update in Classification and Identification of Motif Conservation 
PLoS ONE  2013;8(5):e63098.
The non-structural protein 1 (NS1) of influenza A virus (IAV), coded by its third most diverse gene, interacts with multiple molecules within infected cells. NS1 is involved in host immune response regulation and is a potential contributor to the virus host range. Early phylogenetic analyses using 50 sequences led to the classification of NS1 gene variants into groups (alleles) A and B. We reanalyzed NS1 diversity using 14,716 complete NS IAV sequences, downloaded from public databases, without host bias. Removal of sequence redundancy and further structured clustering at 96.8% amino acid similarity produced 415 clusters that enhanced our capability to detect distinct subgroups and lineages, which were assigned a numerical nomenclature. Maximum likelihood phylogenetic reconstruction using RNA sequences indicated the previously identified deep branching separating group A from group B, with five distinct subgroups within A as well as two and five lineages within the A4 and A5 subgroups, respectively. Our classification model proposes that sequence patterns in thirteen amino acid positions are sufficient to fit >99.9% of all currently available NS1 sequences into the A subgroups/lineages or the B group. This classification reduces host and virus bias through the prioritization of NS1 RNA phylogenetics over host or virus phenetics. We found significant sequence conservation within the subgroups and lineages with characteristic patterns of functional motifs, such as the differential binding of CPSF30 and crk/crkL or the availability of a C-terminal PDZ-binding motif. To understand selection pressures and evolution acting on NS1, it is necessary to organize the available data. This updated classification may help to clarify and organize the study of NS1 interactions and pathogenic differences and allow the drawing of further functional inferences on sequences in each group, subgroup and lineage rather than on a strain-by-strain basis.
PMCID: PMC3646732  PMID: 23667580
22.  Cytokines related to MMP-11 expression by inflammatory cells and breast cancer metastasis 
Oncoimmunology  2013;2(5):e24010.
Breast tumors infiltrated by matrix metalloprotease 11 (MMP-11)+ mononuclear inflammatory cells are prone to form metastases; express high levels of interleukin (IL)-1, IL-5, IL-6, IL-17, interferon β (IFNβ) and NFκB; and exhibit an increased CD68+/(CD3+CD20+) cell ratio at their invasive front. These factors, which are implicated in the crosstalk between tumors and their inflammatory microenvironment, may emerge as attractive prognostic factors and therapeutic targets.
PMCID: PMC3667897  PMID: 23762791
inflammation; interleukins; matrix metalloprotease 11; metastasis
23.  Surname and Y chromosome in Southern Europe: a case study with Colom/Colombo 
According to most historians, Christopher Columbus was born in Genoa, Italy. However, based on some key facts in the discoverer's biography, as well as in the linguistic analysis of his texts, some historians and linguists believe that Columbus could have been of Catalan origin. A Ligurian Columbus would have carried the Colombo surname, whereas he would have been called Colom if he were Catalan. In order to test whether it would be possible to discriminate between a Ligurian or a Catalan origin were Columbus' Y-chromosome haplotype to be retrieved, we genotyped 17 Y-chromosome STRs in 238 Spanish (from Catalonia, Valencia, and the Balearic Islands) and French Colom men, and 114 North Italian Colombo (from Liguria, Lombardy, and Piedmont). The Italian samples and, in particular, the Lombard Colombos were genetically as diverse as the general population, and we found little evidence of clusters of haplotypes that could indicate descent from a single founder. Colombo is actually the most frequent surname in Lombardy, where foundlings and orphans used to be given the surname Colombo. By contrast, Y-chromosome diversity was reduced in the Iberian Colom, where most of the men had Y chromosomes belonging to a few lineages. This implies that a positive identification would be more likely if Columbus were of Catalan descent. In this study, we have shown the diverse dynamics of two surnames linked by their etymology, in what is, to the best of our knowledge, the first genetic analysis of a surname in Southern Europe.
PMCID: PMC3260934  PMID: 21847141
surnames; Y chromosome; Christopher Columbus
24.  Impact of CD68/(CD3+CD20) Ratio at the Invasive Front of Primary Tumors on Distant Metastasis Development in Breast Cancer 
PLoS ONE  2012;7(12):e52796.
Tumors are infiltrated by macrophages, T and B-lymphocytes, which may favor tumor development by promoting angiogenesis, growth and invasion. The aim of this study was to investigate the clinical relevance of the relative amount of macrophages (CD68+), T-cells (CD3+) and B-cells (CD20+) at the invasive front of breast carcinomas, and the expression of matrix metalloproteases (MMPs) and their inhibitors (TIMPs) either at the invasive front or at the tumor center. We performed an immunohistochemical study counting CD3, CD20 and CD68 positive cells at the invasive front, in 102 breast carcinomas. Also, tissue sections were stained with MMP-2, -9, -11, -14 and TIMP-2 antibodies, and immunoreactivity location, percentage of reactive area and intensity were determined at the invasive front and at the tumor center. The results showed that an increased CD68 count and CD68/(CD3+CD20) ratio were directly associated with both MMP-11 and TIMP-2 expression by mononuclear inflammatory cells at the tumor center (p = 0.041 and p = 0.025 for CD68 count and p = 0.001 and p = 0.045 for ratio, respectively for MMP-11 and TIMP-2). In addition, a high CD68/(CD3+CD20) ratio (>0.05) was directly associated with a higher probability of shortened relapse-free survival. Multivariate analysis revealed that CD68/(CD3+CD20) ratio was an independent factor associated with distant relapse-free survival (RR: 2.54, CI: (1.23–5.24), p<0.01). Therefore, CD68/(CD3+CD20) ratio at the invasive front could be used as an important prognostic marker.
PMCID: PMC3530508  PMID: 23300781
25.  Relationship between the Inflammatory Molecular Profile of Breast Carcinomas and Distant Metastasis Development 
PLoS ONE  2012;7(11):e49047.
Inflammatory conditions may promote tumor progression and aggressiveness. In previous reports, we found a group of breast cancer tumors characterized by metalloprotease-11 (MMP-11) expression by intratumoral mononuclear inflammatory cells (MICs), which was associated with distant metastasis development. Thus, in the present study we evaluated the relationship between MMP-11 expression by MICs, distant metastasis development, and a wide panel of inflammatory factors in breast carcinoma. In an initial approach, we analyzed 65 factors associated with tumor progression and inflammation, in a tumor population classified in good or bad prognosis, based on MMP-11 expression by intratumoral MICs. The most differentially expressed factors were then analyzed in a wider tumor population classified according to MMP-11 expression by MICs and also according to metastasis development. These analyses were carried out by Real-time PCR. The results showed that of the 65 starting factors analyzed, those related with MMP-11 expression by MICs were: IL-1, −5, −6, −8, −17, −18, MMP-1, TIMP-1, ADAM-8, −10, −15, −23, ADAMTS-1, −2, −15, Annexin A2, IFNβ, Claudin-3, CCL-3, MyD88, IRAK-4 and NFκB. Of them, factors more differentially expressed between both groups of tumors were IL-1, IL-5, IL-6, IL-17, IFNβ and NFκB. Thereafter, we confirmed in the wider tumor population, that there is a higher expression of those factors in tumors infiltrated by MMP-11 positive MICs. Altogether these results indicate that tumors developing worse prognosis and identified by MMP-11 expression by intratumoral MICs, shows an up-regulation of inflammatory-related genes.
PMCID: PMC3493514  PMID: 23145063

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