Publications by authors named "Carlos Carpio"

42 Publications

The demand for a COVID-19 vaccine in Kenya.

Hum Vaccin Immunother 2021 Jul 9:1-9. Epub 2021 Jul 9.

Department of Socio-economics and Policy Development, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya.

The goal of achieving herd immunity to the coronavirus requires high vaccination acceptance levels on the part of the population. The objectives of this study were to: 1) Measure individuals' willingness to pay (WTP) for a COVID-19 vaccine in Kenya; 2) evaluate the effect of vaccine characteristics (duration of protection and efficacy) and individuals' socioeconomic variables on WTP, and 3) estimate the aggregate demand and economic value of a COVID-19 vaccine. The contingent valuation (CV) method was used as the basis for the analyses. Data for this study were obtained from a survey of 1,050 individuals in Kenya conducted from April 7 to April 15, 2020. The survey included CV questions using a double-bounded dichotomous choice format. Results reveal that most of the individuals in Kenya (at least 96%) were willing to accept a COVID-19 vaccine. Approximately 80% of individuals were willing to pay a positive amount. Conservative estimates of individuals' mean WTP for the vaccine range from USD 49.81 to USD 68.25 (depending on vaccine characteristics). Both vaccine duration of protection and efficacy were found to influence WTP ( < .10). The perceived probability of being hospitalized, age, gender, education, location and region of residence, and household income were also found to be associated with WTP for the vaccine ( < .10). In conclusion, the COVID-19 vaccine is highly valued and accepted by the Kenyan population; however, a high percent of the population is unwilling to pay for it or is only willing to pay a low price.
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http://dx.doi.org/10.1080/21645515.2021.1938494DOI Listing
July 2021

Inhaled bronchodilators use and clinical course of adult inpatients with Covid-19 pneumonia in Spain: A retrospective cohort study.

Pulm Pharmacol Ther 2021 Jun 12;69:102007. Epub 2021 Jun 12.

Pneumology Department, La Paz University Hospital, IdiPAZ, Madrid, Spain.

Background: In the current coronavirus health crisis, inhaled bronchodilators(IB) have been suggested as a possible treatment for patients hospitalized. Patients with evidence of Covid-19 pneumonia worldwide have been prescribed these medications as part of therapy for the disease, an indication for which this medications could be ineffective taken on account the pathophysiology and mechanisms of disease progression.

Objective: The main objective was to evaluate whether there is an association between IB use and length of stay. Primary end points were the number of days that a patient stayed in the hospital and death as a final event in a time to event analysis. Pneumonia severity, oxygen requirement, involved drugs, comorbidity, historical or current respiratory diagnoses and other drugs prescribed to treat coronavirus pneumonia were also evaluated.

Methods: A descriptive, observational, cross-sectional study was performed in this tertiary hospital in Madrid (Spain). Data were obtained regarding patients hospitalized with Covid-19, excluding those who were intubated. The primary and secondary outcomes such as duration of hospitalization and death were compared in patients who received IB with those in patients who did not.

Results: 327 patients were evaluated, mean age was 64.4 ± 15.8 years. Median length of hospitalization stay was 10 days. Of them 292 (89.3%) overcame the disease, the remaining 35 died. Patients who had received IB did not have less mortality rate (odds ratio 0.839; 95% CI: 0.401 to 1.752) and less hospitalization period when compared with patients who did not received IB (odds ratio 1.280; 95% CI: 0.813 to 2.027). There was no significant association between IB use and recovery or death. Hypertension and diabetes were the most common comorbidities. The prevalence of chronic respiratory disease in our cohort was low (21.1%). Anticholinergics were the IB more frequently prescribed for Covid-19 pneumonia. Better response in patients treated with inhaled corticosteroids was not observed.

Conclusion: Off-label indication of inhaled-bronchodilators for Covid-19 patients are common in admitted patients. Taken on account our results, the use of IB for coronavirus pneumonia apparently is not associated with a significantly patient's improvement. Our study confirms the hypothesis that inhaled bronchodilators do not improve clinical outcomes or reduce the risk of Covid-19 mortality. This could be due to the fact that the virus mainly affects the lung parenchyma and the pulmonary vasculature and probably not the airway. More researches are necessary in order to fill the gap in evidence for this new indication.
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http://dx.doi.org/10.1016/j.pupt.2021.102007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196225PMC
June 2021

Quinoa in Ecuador: Recent Advances under Global Expansion.

Plants (Basel) 2021 Feb 4;10(2). Epub 2021 Feb 4.

Sustainable Seed Systems Lab, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA 99164-6420, USA.

Quinoa is a highly diverse crop domesticated in the Andean region of South America with broad adaptation to a wide range of marginal environments. Quinoa has garnered interest worldwide due to its nutritional and health benefits. Over the last decade, quinoa production has expanded outside of the Andean region, prompting multiple studies investigating the potential for quinoa cultivation in novel environments. Currently, quinoa is grown in countries spanning five continents, including North America, Europe, Asia, Africa, and Oceania. Here, we update the advances of quinoa research in Ecuador across different topics, including (a) current quinoa production situation with a focus on breeding progress, (b) traditional seed production, and (c) the impact of the work of the nongovernment organization "European Committee for Training and Agriculture" with quinoa farmers in Chimborazo province. Additionally, we discuss genetic diversity, primary pests and diseases, actions for adapting quinoa to tropical areas, and recent innovations in quinoa processing in Ecuador. Finally, we report a case study describing a participatory breeding project between Washington State University and the Association of Andean Seed and Nutritional Food Producers Mushuk Yuyay in the province of Cañar.
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http://dx.doi.org/10.3390/plants10020298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7915685PMC
February 2021

Psycho-demographic profile in severe asthma and effect of emotional mood disorders and hyperventilation syndrome on quality of life.

BMC Psychol 2021 Jan 6;9(1). Epub 2021 Jan 6.

Pneumology, Hospital Universitario La Paz, Universidad Autónoma de Madrid, CIBERES, Madrid, Spain.

Background: Severe asthma affects a small population but carries a high psychopathological risk. Therefore, the psychodemographic profile of these patients is of interest. A substantial prevalence of anxiety, depression, alexithymia and hyperventilation syndrome in severe asthma is known, but contradictory results have been observed. These factors can also affect patients' quality of life. For this reasons, our purpose is to evaluate the psychodemographic profile of patients with severe asthma and assess the prevalence of anxiety, depression, alexithymia and hyperventilation syndrome and their impact on the quality of life of patients with severe asthma.

Methods: A cross-sectional study of 63 patients with severe asthma. Their psychodemographic profile was evaluated using the Hospital Anxiety and Depression Scale (HADS), Toronto Alexithymia Scale (TAS-20), Nijmegen questionnaire and Asthma Control Test (ACT) to determine the state of anxiety and depression, alexithymia, hyperventilation syndrome and control of asthma, respectively. Quality of life was assessed with the Mini Asthma Quality of Life Questionnaire (Mini-AQLQ).

Results: The mean age was 60 ± 13.6 years. Personal psychopathological histories were found in 65.1% of participants, and 8% reported previous suicidal attempts. The rate of anxiety and/or depression (HADS ≥ 11) was 68.3%. These patients present higher scores on the TAS-20 (p < 0.001) for the level of dyspnea (p = 0.021), and for emotional function (p = 0.017) on the Mini-AQLQ, compared with patients without anxiety or depression. Alexithymia (TAS-20 ≥ 61) was observed in 42.9% of patients; these patients were older (p = 0.037) and had a higher HADS score (p = 0.019) than patients with asthma without alexithymia. On the other hand, patients with hyperventilation syndrome (Nijmegen ≥ 23) scored higher on the HADS (p < 0.05), on the Mini-AQLQ (p = 0.002) and on the TAS-20 (p = 0.044) than the group without hyperventilation syndrome. Quality of life was related to anxiety-depression symptomatology (r =  - 0.302; p = 0.016) and alexithymia (r =  - 0.264; p = 0.036). Finally, the Mini-AQLQ total score was associated with the Nijmegen questionnaire total score (r =  - 0.317; p = 0.011), and the activity limitation domain of the Mini-AQLQ correlated with the ACT total score (r = 0.288; p = 0.022).

Conclusions: The rate of anxiety, depression, alexithymia and hyperventilation syndrome is high in patients with severe asthma. Each of these factors is associated with a poor quality of life.
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http://dx.doi.org/10.1186/s40359-020-00498-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788781PMC
January 2021

The demand for a COVID-19 vaccine in Ecuador.

Vaccine 2020 12 6;38(51):8090-8098. Epub 2020 Nov 6.

Department of Business Administration, Ana G. Mendez University, San Juan 00926, PR, USA.

In Latin America, the country of Ecuador was one of the first and most severely affected by the COVID-19 pandemic. This study aimed to evaluate the demand for a COVID-19 vaccine in Ecuador by estimating individuals' willingness to pay (WTP) for the vaccine, and by assessing the effect of vaccine attributes (duration of protection and efficacy) and individuals' characteristics on this valuation. The sample used (N = 1,050) was obtained through an online survey conducted from April 2 to April 7, 2020. Two levels of vaccine efficacy (70% and 98%) and two levels of vaccine duration of protection (1 and 20 years) were considered. The willingness to pay estimates were obtained using a double-bounded dichotomous-choice contingent valuation format. Survey results show that a very large proportion of individuals (at least 97%) were willing to accept a COVID-19 vaccine, and at least 85% of individuals were willing to pay a positive amount for that vaccine. Conservative estimates of the average WTP values ranged from USD 147.61 to 196.65 and the median WTP from USD 76.9 to 102.5. Only the duration of protection was found to influence individuals' WTP for the vaccine (p < 0.01). On average, respondents were willing to pay 30% more for a COVID-19 vaccine with 20 years of protection relative to the vaccine with 1 year of protection. Regression results show that WTP for the vaccine was associated with income, employment status, the perceived probability of needing hospitalization if contracting the virus causing COVID-19, and region of residence.
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http://dx.doi.org/10.1016/j.vaccine.2020.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7832521PMC
December 2020

Comparison between Experience-Based and Household-Undernourishment Food Security Indicators: A Cautionary Tale.

Nutrients 2020 Oct 29;12(11). Epub 2020 Oct 29.

Department of Agricultural and Applied Economics, Texas Tech University, Lubbock, TX 79409, USA.

Food security is a multi-dimensional concept that requires multiple indicators to measure it correctly; however, single food security indicators are often used individually or interchangeably. The misinterpretation of individual food security indicators can have important implications for policy design and implementation. The general objective of this paper is to show the discrepancies that may arise when using two different food security indicators that operate in the same dimension of the food security concept and yield the same outcome (food security status of the household) in three of the scenarios that they might be used: (1) for measuring the prevalence of food insecurity, (2) for understanding its drivers, and (3) for estimating the potential impact of a policy. The specific objectives of this paper are (1) to measure and compare the prevalence of food insecurity in a country using the Latin America Food Security Scale (ELCSA, by its acronym in Spanish) and the household undernourishment indicator, (2) to compare the factors associated with households' food security status using the two indicators, and (3) to assess the potential use of the two indicators for ex ante policy analysis. Data for the study comes from the 2011 Survey of Living Standards from Guatemala, which collected all the data for estimating the ELCSA and the household level data required for calculating the household undernourishment indicator. Our results indicate considerable differences in the estimated prevalence of food insecurity at the national and regional levels using the two alternative indicators, with ELCSA resulting in higher estimates. Logistic regression models estimated to assess and identify household food insecurity drivers also found large differences in both the direction and magnitude of factors affecting food insecurity using the alternative food security indicators. Finally, the magnitude of the simulated impact of a cash transfer policy varied depending on the food indicator used.
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http://dx.doi.org/10.3390/nu12113307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7692183PMC
October 2020

The effect of time use and food cost on dietary quality.

Public Health Nutr 2020 12 13;23(18):3284-3294. Epub 2020 Jul 13.

Department of Nutritional Sciences, College of Human Sciences, Texas Tech University, Lubbock, TX, USA.

Objective: To develop a questionnaire to measure food nutrition, food expenditures and time spent in food-related activities; and to assess the association between diet quality, time spent in food-related activities and food expenditures using data from a pilot study.

Design: Cross-sectional study. Multiple linear regression models were used to analyse participants' survey response behaviours and the relationship between food nutritional quality and time and money expenditures.

Setting: Online survey using Qualtrics software in a public university located in West Texas, USA.

Participants: Faculty and staff aged 18 years and older from a public university located in West Texas, USA.

Results: Combining questions from three survey instruments that collect data on food nutrition, food expenditures and time spent in food-related activities resulted in a thirty-page survey instrument. The median completion time of the survey instrument was about 30 min. Preliminary results suggest that time and money expenditures are associated with food quality but that their role is small relative to sociodemographic characteristics such as race and gender.

Conclusions: Time and money expenditures are associated with food quality but their role is small relative to sociodemographic characteristics such as race and gender.
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http://dx.doi.org/10.1017/S1368980020001615DOI Listing
December 2020

Effects of Aqueous Extracts from Amazon Plants on Plutella xylostella (Lepidoptera: Plutellidae) and Brevicoryne brassicae (Homoptera: Aphididae) in Laboratory, Semifield, and field trials.

J Insect Sci 2019 Sep;19(5)

SVeB-Dept. of Life Sciences and Biotechnology, University of Ferrara, p.le Chiappini, 2, Ferrara, Italy.

We evaluated the insecticide activities of aqueous extracts of five species of plants from the Ecuadorian Amazon (Deguelia utilis (ACSm.) AMGAZEVEDO (Leguminosae: Papilionoideae), Xanthosoma purpuratum K. Krause (Alismatales: Araceae), Clibadium sp. (Asteracea: Asterales), Witheringia solanacea L'Hér (Solanales: Solanaceae), and Dieffenbachia costata H. Karst. ex Schott (Alismatales: Araceae)) plus Cymbopogon citratus Stapf. (Poales: Poaceae) under laboratory, open-field conditions in Plutella xylostella L. (diamondback moth), and semifield conditions in Brevicoryne brassicae L. Tap water was used as a negative control, and synthetic insecticides were used as positive controls. In a laboratory bioassay, aqueous extracts of D. utilis resulted in P. xylostella larval mortality. In contrast to chlorpyrifos, all botanicals were oviposition deterrents. All extracts except Clibadium sp. decreased leaf consumption by P. xylostella larvae. In semifield experiments, D. utilis, Clibadium sp., D. costata, and X. purpuratum initially controlled the population of B. brassicae, but 7 d after application, all botanicals except the D. utilis lost their ability to control the pest. In field experiments on broccoli crops in both dry and rainy seasons, the extracts did not control the abundance of P. xylostella, where as a mixture of two insecticides (chlorpyrifos + lambda cyhalothrin) did. These results show some incongruences from laboratory to semifield and field conditions, indicating that more studies, including the identification of the chemicals responsible for the biological activity, its stability, and the effects of chemotypes on insecticidal activity, are needed to understand the potential of these plant species as botanical insecticides.
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http://dx.doi.org/10.1093/jisesa/iez068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6794192PMC
September 2019

The effect of 'Traffic-Light' nutritional labelling in carbonated soft drink purchases in Ecuador.

PLoS One 2019 3;14(10):e0222866. Epub 2019 Oct 3.

Department of Animal and Food Science, Texas Tech University, Lubbock, TX, United States of America.

Overweight and obesity have become global concerns in developed and developing countries due to their rise in recent years and their association with the prevalence of non-communicable diseases including diabetes, hypertension and cardiovascular diseases. In fact, it is estimated that roughly 39% of adults worldwide are overweight and 13% are obese. Ecuador is an example of a developing country concerned with the overweight and obesity problem, where it is estimated that 30% of children, 26% of teenagers and 63% of adults are either overweight or obese and where 1 in 4 deaths are attributed to chronic diseases. To address the overweight and obesity problem via the promotion of healthy eating habits, in 2013 the country approved technical regulation for the labelling of packed processed food products. The regulation included a mandatory traffic-light (TL) supplemental nutritional information labelling system to be displayed on the package of all processed foods for sale in the country. This new labelling system displays a traffic light panel for the product content of sugar, fat and salt in addition to the traditional nutrient declaration label. The objective of this paper was to evaluate the effect of the TL supplemental nutritional information on consumers' buying behavior in Ecuador. More specifically, we concentrated on the purchasing behavior of carbonated soft drinks. For our analysis, we used monthly aggregated purchase data (total expenditures, quantities and average prices) of carbonated soft drinks from January 2013 to December 2015 obtained from Kantar World Panel-Ecuador. We estimated a non-linear Almost Ideal Demand System where we model the demand for high sugar and low sugar carbonated soft drinks. We found that the introduction of the traffic light supplemental nutrition labelling did not have the expected effect of reducing purchases of carbonated soft drinks during its first year of implementation, especially those high in sugar. Additionally, we found that lower income-status households tend to spend more on and consume more calories from CSD than households with higher socio-economic status. Finally, we identified that over time purchases of high sugar soft drinks decreased while purchases of low and no sugar soft drinks increased. Beyond our contribution of evaluating the effect of the traffic light on the purchases of carbonated soft drinks, we also estimated price and income elasticities of carbonated soft drinks which can be useful in the evaluation of fiscal policies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222866PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776320PMC
March 2020

[Effect of traffic-light labeling on nutritional content and on consumption of carbonated beverages in EcuadorEfeito da rotulagem nutricional com modelo de semáforo no consumo de refrigerantes no Equador].

Rev Panam Salud Publica 2018 27;42:e177. Epub 2018 Dec 27.

Universidad San Francisco de Quito, Quito, Ecuador.

Objective: To evaluate the effect of "traffic-light" nutritional labeling on the purchase of soft drinks and on their nutritional content in Ecuador.

Methods: Two databases were used: the first was provided by Ecuador's National Agency for Health Regulation, Control, and Surveillance; the second was obtained from the international market research company Kantar World Panel. A before/after study was conducted of introducing traffic-light labeling, using Student's t-tests to evaluate changes in average nutritional content and the purchase of soft drinks. Multiple linear regression methods were used to evaluate changes in purchases resulting from the introduction of traffic-light labeling.

Results: After labeling, average per capita consumption of soft drinks declined by 0.003 L/month--a small change with respect to average per capita consumption of 1.678 L/month. The results of the Student's t-tests indicated that this difference was not statistically significant. Furthermore, the regression analyses found no empirical evidence that traffic-light labeling affected soft drink consumption. With regard to sugar content, an average reduction of 0.93 gm/100 ml of beverage was observed.

Conclusions: No empirical evidence was found that implementation of traffic-light labeling changed soft-drink purchase habits in Ecuador, but there is evidence that it reduced sugar content in carbonated beverages in the country.
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http://dx.doi.org/10.26633/RPSP.2018.177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398322PMC
December 2018

Facilitation costs and benefits function simultaneously on stress gradients for animals.

Proc Biol Sci 2018 08 22;285(1885). Epub 2018 Aug 22.

Department of Biology, York University, Toronto, Ontario, Canada.

Understanding the variation in species interactions along environmental stress gradients is crucial for making robust ecological predictions about community responses to changing environmental conditions. The facilitation-competition framework has provided a strong basis for predictions (e.g. the stress-gradient hypothesis, SGH), yet the mechanisms behind patterns in animal interactions on stress gradients are poorly explored in particular for mobile animals. Here, we proposed a conceptual framework modelling changes in facilitation costs and benefits along stress gradients and experimentally tested this framework by measuring fitness outcomes of benefactor-beneficiary interactions across resource quality levels. Three arthropod consumer models from a broad array of environmental conditions were used including aquatic detritivores, potato moths and rainforest carrion beetles. We detected a shift to more positive interactions at increasing levels of stress thereby supporting the application of the SGH to mobile animals. While most benefactors paid no significant cost of facilitation, an increase in potato moth beneficiary's growth at high resource stress triggered costs for benefactors. This study is the first to experimentally show that both costs and benefits function simultaneously on stress gradients for animals. The proposed conceptual framework could guide future studies examining species interaction outcomes for both animals and plants in an increasingly stressed world.
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http://dx.doi.org/10.1098/rspb.2018.0983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125904PMC
August 2018

Obstructive Sleep Apnea Monocytes Exhibit High Levels of Vascular Endothelial Growth Factor Secretion, Augmenting Tumor Progression.

Mediators Inflamm 2018 28;2018:7373921. Epub 2018 May 28.

The Innate Immune Response Group, Tumor Immunology Lab, IdiPAZ, La Paz University Hospital, Madrid, Spain.

Obstructive sleep apnea (OSA) is a syndrome characterized by repeated pauses in breathing induced by a partial or complete collapse of the upper airways during sleep. Intermittent hypoxia (IH), a hallmark characteristic of OSA, has been proposed to be a major determinant of cancer development, and patients with OSA are at a higher risk of tumors. Both OSA and healthy monocytes have been found to show enhanced HIF1 expression under IH. Moreover, these cells under IH polarize toward a tumor-promoting phenotype in a HIF1-dependent manner and influence tumor growth via vascular endothelial growth factor (VEGF). Monocytes from patients with OSA increased the tumor-induced microenvironment and exhibited an impaired cytotoxicity in a 3D tumor model as a result of the increased HIF1 secretion. Adequate oxygen restoration both (under continuous positive airway pressure treatment, CPAP) and leads the monocytes to revert the tumor-promoting phenotype, demonstrating the plasticity of the innate immune system and the oxygen recovery relevance in this context.
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http://dx.doi.org/10.1155/2018/7373921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994578PMC
October 2018

Monocytes inhibit NK activity TGF-β in patients with obstructive sleep apnoea.

Eur Respir J 2017 06 15;49(6). Epub 2017 Jun 15.

The Innate Immune Response Group, IdiPAZ, La Paz University Hospital, Madrid, Spain

Obstructive sleep apnoea (OSA) is associated with cancer incidence and mortality. The contribution of the immune system appears to be crucial; however, the potential role of monocytes and natural killer (NK) cells remains unclear.Quantitative reverse transcriptase PCR, flow cytometry and assays were used to analyse the phenotype and immune response activity in 92 patients with OSA (60 recently diagnosed untreated patients and 32 patients after 6 months of treatment with continuous positive airway pressure (CPAP)) and 29 healthy volunteers (HV).We determined that monocytes in patients with OSA exhibit an immunosuppressive phenotype, including surface expression of glycoprotein-A repetitions predominant protein (GARP) and transforming growth factor-β (TGF-β), in contrast to those from the HV and CPAP groups. High levels of TGF-β were detected in OSA sera. TGF-β release by GARP monocytes impaired NK cytotoxicity and maturation. This altered phenotype correlated with the hypoxic severity clinical score (CT90). Reoxygenation eventually restored the altered phenotypes and cytotoxicity.This study demonstrates that GARP monocytes from untreated patients with OSA have an NK-suppressing role through their release of TGF-β. Our findings show that monocyte plasticity immunomodulates NK activity in this pathology, suggesting a potential role in cancer incidence.
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http://dx.doi.org/10.1183/13993003.02456-2016DOI Listing
June 2017

[Massive cardiac lipomatosis, an autopsy finding in a patient with sudden death].

Med Clin (Barc) 2016 Jun 1;146(12):541-3. Epub 2016 May 1.

Servicio de Neumología, Hospital Universitario La Paz, Instituto de Investigación Hospital Universitario La Paz (IdiPaz), Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Universidad Autónoma de Madrid, Madrid, España.

The fat replacement of myocardial cells is a degenerative process that usually affects the right ventricle and is found in 50% of the elderly. The problem arises when this degeneration occurs to a massive degree, a differential diagnosis with other pathologies being necessary. We present the case of a patient who died suddenly and a massive cardiac lipomatosis was found on autopsy, as the only explanation of the outcome.
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http://dx.doi.org/10.1016/j.medcli.2016.03.022DOI Listing
June 2016

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Proteins 2016 09 1;84 Suppl 1:323-48. Epub 2016 Jun 1.

Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. Proteins 2016; 84(Suppl 1):323-348. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/prot.25007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136PMC
September 2016

Systemic inflammation and higher perception of dyspnea mimicking asthma in obese subjects.

J Allergy Clin Immunol 2016 Mar 5;137(3):718-26.e4. Epub 2016 Jan 5.

Servicio de Neumología, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Universidad Autónoma de Madrid, Madrid, Spain. Electronic address:

Background: There are a variable number of obese subjects with self-reported diagnosis of asthma but without current or previous evidence of airflow limitation, bronchial reversibility, or airway hyperresponsiveness (misdiagnosed asthma). However, the mechanisms of asthma-like symptoms in obesity remain unclear.

Objectives: We sought to evaluate the perception of dyspnea during bronchial challenge and exercise testing in obese patients with asthma and misdiagnosed asthma compared with obese control subjects to identify the mechanisms of asthma-like symptoms in obesity.

Methods: In a cross-sectional study we included obese subjects with asthma (n = 25), misdiagnosed asthma (n = 23), and no asthma or respiratory symptoms (n = 27). Spirometry, lung volumes, exhaled nitric oxide levels, and systemic biomarker levels were measured. Dyspnea scores during adenosine bronchial challenge and incremental exercise testing were obtained.

Results: During bronchial challenge, patients with asthma or misdiagnosed asthma reached a higher Borg-FEV1 slope than control subjects. Moreover, maximum dyspnea and the Borg-oxygen uptake (V'O2) slope were significantly greater during exercise in subjects with asthma or misdiagnosed asthma than in control subjects. The maximum dyspnea achieved during bronchial challenge correlated with IL-1β levels, whereas peak respiratory frequency, ventilatory equivalent for CO2, and IL-6 and IL-1β levels were independent predictors of the Borg-V'O2 slope during exercise (r(2) = 0.853, P < .001).

Conclusions: A false diagnosis of asthma (misdiagnosed asthma) in obese subjects is attributable to an increased perception of dyspnea, which, during exercise, is mainly associated with systemic inflammation and excessive ventilation for metabolic demands.
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http://dx.doi.org/10.1016/j.jaci.2015.11.010DOI Listing
March 2016

[EFFECTS OF WEIGHT LOSS AFTER BARIATRIC SURGERY ON PULMONARY FUNCTION TESTS AND OBSTRUCTIVE SLEEP APNEA IN MORBIDLY OBESE WOMEN].

Nutr Hosp 2015 Sep 1;32(3):1050-5. Epub 2015 Sep 1.

Servicio de Medicina Intensiva. Hospital Universitario La Paz. IdiPAZ. Universidad Autónoma de Madrid, España..

Introduction: obesity impacts on respiratory function and also it acts as a risk factor for obstructive sleep apnea (OSA).

Aims: to study the effects of bariatric surgery on pulmonary function tests and on OSA in morbidly obese women over 4 years.

Methods: fifteen morbidly obese women (mean body mass index [BMI] 50.52 ± 12.71 kg.m-2, mean age 40.13 ± 10.06 years) underwent pulmonary function tests (PFT) in two opportunities (before and after weight loss surgery). PFT included spirometry, body plethysmography and measure of maximal inspiratory mouth pressure (PImax) and of tension-time index for inspiratory muscles. Also, in both opportunities, resting arterial blood gas tensions were evaluated and a full night sleep register was performed.

Results: BMI significantly decreased after bariatric surgery (-44.07 kg.m-2 [CI 95% -38.32 - -49.81]). Also, there was a significantly increase in forced expiratory volume in 1 second (FEV1) (p < 0.01), forced vital capacity (FVC) (p < 0.01), expiratory reserve volume (ERV) (p = 0.040), functional residual capacity (FRC) (p = 0.009) and a decline in airways resistance (Raw) (p = 0.018). Concerning sleep registers, apnea hypopnea index (p = 0.001) and desaturation index (p = 0.001) were also reduced after weight loss. Improve in ERV had a significant correlation with weight loss (r = 0.774, p = 0.024). Conclussions: pulmonary function tests and apnea hypopnea index improve after bariatric surgery in mor bidly obese women. Improvement of ERV is well correlated with weight loss.
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http://dx.doi.org/10.3305/nh.2015.32.3.9487DOI Listing
September 2015

Changes in structural lung disease in cystic fibrosis children over 4 years as evaluated by high-resolution computed tomography.

Eur Radiol 2015 Dec 1;25(12):3577-85. Epub 2015 May 1.

Department of Radiology, University Hospital La Princesa, Madrid, Spain.

Objectives: To compare the worsening of structural lung disease on high-resolution computed tomography (HRCT) with changes in spirometry results in cystic fibrosis (CF) patients, and analyse factors associated with the worsening of structural lung disease over time.

Methods: A total of 31 CF subjects (mean age 11.03 ± 3.67 years old) were prospectively evaluated by two HRCT and spirometry tests performed 4 years apart. HRCT abnormalities were scored using the Bhalla scoring system. Comparisons between changes on HRCT and spirometry were made for all patients, and also for groups categorized by age, sex, genotypic alterations and lung obstruction.

Results: The mean HRCT Bhalla scoring, forced expiratory volume in 1 s (FEV1 %pred.) and forced vital capacity (FVC %pred.) were 7.92 ± 3.59, 87.76 ± 20.52 and 96.54 ± 15.12, respectively. There was a significant deterioration in the Bhalla score (p < 0.01) and in certain categories: severity of bronchiectasis, peribronchial thickening, mucous plugging and bronchial divisions. Females had a more pronounced worsening of the Bhalla score than males (p = 0.048). No change over time was found in FEV1 and FVC. Only sex was associated with a deterioration in HRCT.

Conclusions: HRCT Bhalla scoring changes statistically significantly over 4 years, but spirometry results do not. Worsening on HRCT is more evident in females.

Key Points: • HRCT Bhalla scoring changes significantly over 4 years, spirometry results do not. • Females experience faster respiratory deterioration than males. • Spirometry results are not associated with deterioration in HRCT.
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http://dx.doi.org/10.1007/s00330-015-3782-4DOI Listing
December 2015

THE ANATOMICAL MUSEUM PEDRO ARA.

Med Secoli 2015 ;27(2):733-6

The contribute is aimed to shed light on the history of the Anatomical Museum Pedro Ara since his foundation in 1878. Particularly, it describes the activity of Pedro Ara in preparing the anatomical specimens, which constitute the original collection of the Museum.
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March 2016

[Changes in lung function testing associated with obesity].

Nutr Hosp 2014 Nov 1;30(5):1054-62. Epub 2014 Nov 1.

Servicio de Neumología. Hospital Universitario La Paz. Instituto de Investigación Hospital Universitario La Paz (IdiPAZ). Universidad Autónoma de Madrid. España..

Excess bodyweight has an important impact on the physiology of breathing. In fact, it affects resting lung volumes and exercise capacity. These effects appear as a consequence of ventilatory and inflammatory changes commonly associated to obesity. As a result, obese individuals have a rapid and shallow pattern of breathing, their respiratory compliance is reduced and the airway resistance tends to be higher. However, with respect to aerobic capacity, contradictory results have been reported depending on the way peak oxygen uptake is expressed. Moreover, the inability of this population to achieve maximal efforts during exercise testing also affects their cardiorespiratory fitness.
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http://dx.doi.org/10.3305/nh.2014.30.5.8042DOI Listing
November 2014

Evolution of the COPD Assessment Test score during chronic obstructive pulmonary disease exacerbations: determinants and prognostic value.

Can Respir J 2013 Sep-Oct;20(5):e92-7

Background: An adequate evaluation of exacerbations is a primary objective in managing patients with chronic obstructive pulmonary disease (COPD).

Objectives: To define the profile of health status recovery during severe exacerbations of COPD using the COPD Assessment Test (CAT) questionnaire and to evaluate its prognostic value.

Methods: Forty-five patients with previous COPD diagnoses who were hospitalized due to severe exacerbation(s) were included in the study. These patients were treated by their respective physicians following current recommendations; health status was assessed daily using the CAT questionnaire. The CAT score, spirometry and recurrent hospitalizations were recorded one and three months after hospital discharge.

Results: Global initiative for chronic Obstructive Lung Disease (GOLD) stage was an independent determinant for increased CAT score during the first days of exacerbation with respect to postexacerbation values. From hospitalization day 5, the CAT score was similar to that obtained in the stable phase. Body mass index, GOLD stage and education level were related to health status recovery pattern. CAT score increase and the area under the curve of CAT recovery were inversely related to the forced expiratory volume in 1 s achieved three months after discharge (r=-0.606; P<0.001 and r=-0.532; P<0.001, respectively). Patients with recurrent hospitalizations showed higher CAT score increases and slower recovery.

Conclusions: The CAT detects early health status improvement during severe COPD exacerbations. Its initial worsening and recovery pattern are related to lung function and recurrent hospitalizations.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810053PMC
http://dx.doi.org/10.1155/2013/398120DOI Listing
June 2014

Epidemiological and Pathogenic Relationship between Sleep Apnea and Ischemic Heart Disease.

Pulm Med 2013 18;2013:405827. Epub 2013 Jun 18.

Servicio de Neumología, Hospital Universitario La Paz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain.

Obstructive sleep apnea is recognized as having high prevalence and causing remarkable cardiovascular risk. Coronary artery disease has been associated with obstructive sleep apnea in many reports. The pathophysiology of coronary artery disease in obstructive sleep apnea patients probably includes the activation of multiple mechanisms, as the sympathetic activity, endothelial dysfunction, atherosclerosis, and systemic hypertension. Moreover, chronic intermittent hypoxia and oxidative stress have an important role in the pathogenesis of coronary disease and are also fundamental to the development of atherosclerosis and other comorbidities present in coronary artery diseases such as lipid metabolic disorders. Interestingly, the prognosis of patients with coronary artery disease has been associated with obstructive sleep apnea and the severity of sleep disordered breathing may have a direct relationship with the morbidity and mortality of patients with coronary diseases. Nevertheless, treatment with CPAP may have important effects, and recent reports have described the benefits of obstructive sleep apnea treatment on the recurrence of acute heart ischaemic events in patients with coronary artery disease.
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http://dx.doi.org/10.1155/2013/405827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703797PMC
July 2013

Size-dependent species removal impairs ecosystem functioning in a large-scale tropical field experiment.

Ecology 2012 Dec;93(12):2615-25

Pontificia Universidad Católica del Ecuador, Facultad de Ciencias Exactas y Naturales, Quito, Ecuador.

A major challenge of ecological research is to assess the functional consequences of species richness loss over time and space in global biodiversity hotspots, where extinctions are happening at an unprecedented rate. To address this issue, greater realism needs to be incorporated into both conceptual and experimental approaches. Here we propose a conceptual model that incorporates body size as a critical aspect of community responses to environmental change, which we tested in the Western Amazonian rain forest, one of the most speciose ecosystems on the planet. We employed an exclosure removal experiment (replicated under 10 microhabitats and four climatic conditions) in which we manipulated access to two types of resource by the whole community of dung and carrion beetles (> 60 species), depending on their size. Our 400 independent measurements revealed that changes in the number of species and functional groups, and temporal patterns in community composition, all affected resource burial rates, a key ecosystem process. Further, the functional contribution of species diversity in each size class was tightly dependent on beetle abundance, and while the role of large species could be performed by abundant smaller ones, and other naturally occurring decomposers, this was not the case when environmental conditions were harsher. These results demonstrate, for the first time in an animal assemblage in a tropical ecosystem, that although species may appear functionally redundant under one set of environmental conditions, many species would be needed to maintain ecosystem functioning at multiple temporal and spatial scales. This highlights the potential fragility of these systems to the ongoing global "Sixth Great Extinction," whose effects are likely to be especially pronounced in the Tropics.
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http://dx.doi.org/10.1890/12-0510.1DOI Listing
December 2012

CPAP effect on recurrent episodes in patients with sleep apnea and myocardial infarction.

Int J Cardiol 2013 Sep 7;168(2):1328-35. Epub 2013 Jan 7.

Servicio de Neumología, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain; CIBER Enfermedades Respiratorias (CIBERES), Spain. Electronic address:

Background: Obstructive sleep apnea (OSA) is linked to increased cardiovascular risk, but the association between OSA and myocardial infarction (MI) remains controversial. Our objectives were to compare the frequency of OSA in patients with acute MI and in a population-based sample of control subjects, and to evaluate the impact of CPAP on recurrent MI and coronary revascularization.

Methods: Case-control study with a 6-year follow-up of the case cohort. 192 acute MI patients and 96 matched control subjects without coronary artery disease (CAD) (ratio 2:1). After overnight polysomnography, CPAP was recommended if apnea-hypopnea index (AHI) ≥ 5, and a mean daily use >3.5h/day was considered necessary to maintain the treatment. Lipids, fasting glucose, blood pressure, spirometry, comorbidity and current treatment were also registered. End-points were recurrent MI or need of revascularization.

Results: OSA was an independent predictor of MI, with odds ratio 4.9 (95% confidence interval [CI] 2.9-8.3, p=0.017). 63 MI patients without OSA, 52 untreated patients with OSA and 71 OSA patients treated with CPAP were included in the follow-up study. After adjustment for confounding factors, treated OSA patients had a lower risk of recurrent MI (adjusted hazard ratio 0.16 [95%CI 0.03-0.76, p=0.021]) and revascularization (adjusted hazard ratio 0.15 [95%CI 0.03-0.79, p=0.025]) than untreated OSA patients, and similar to non-OSA patients.

Conclusion: Mild-severe OSA is an independent risk factor for MI. Risk of recurrent MI and revascularization was lower in OSA patients who tolerated CPAP.
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http://dx.doi.org/10.1016/j.ijcard.2012.12.015DOI Listing
September 2013

Development of a viral biopesticide for the control of the Guatemala potato tuber moth Tecia solanivora.

J Invertebr Pathol 2013 Feb 8;112(2):184-91. Epub 2012 Dec 8.

Pontificia Universidad Católica del Ecuador, Facultad de Ciencias Naturales y Biológicas, Quito, Ecuador.

The Guatemala potato tuber moth Tecia solanivora (Povolny) (Lep. Gelechiidae) is an invasive species from Mesoamerica that has considerably extended its distribution area in recent decades. While this species is considered to be a major potato pest in Venezuela, Colombia, and Ecuador, currently no specific control methods are available for farmers. To address this issue we developed a biopesticide formulation to be used in integrated pest management of T. solanivora, following three steps. First, search for entomopathogenic viruses were carried out through extensive bioprospections in 12 countries worldwide. As a result, new Phthorimaea operculella granulovirus (PhopGV) isolates were found in T. solanivora and five other gelechid species. Second, twenty PhopGV isolates, including both previously known and newly found isolates, were genetically and/or biologically characterized in order to choose the best candidate for a biopesticide formulation. Sequence data were obtained for the ecdysteroid UDP-glucosyltransferase (egt) gene, a single copy gene known to play a role in pathogenicity. Three different sizes (1086, 1305 and 1353 bp) of egt were found among the virus isolates analyzed. Unexpectedly, no obvious correlation between egt size and pathogenicity was found. Bioassays on T. solanivora neonates showed a maximum of a 14-fold difference in pathogenicity among the eight PhopGV isolates tested. The most pathogenic PhopGV isolate, JLZ9f, had a medium lethal concentration (LC(50)) of 10 viral occlusion bodies per square mm of consumed tuber skin. Third, we tested biopesticide dust formulations by mixing a dry carrier (calcium carbonate) with different adjuvants (magnesium chloride or an optical brightener or soya lecithin) and different specific amounts of JLZ9f. During laboratory experiments, satisfactory control of the pest (>98% larva mortality compared to untreated control) was achieved with a formulation containing 10 macerated JLZ9f-dead T. solanivora larvae per kg of calcium carbonate mixed with 50 mL/kg of soya lecithin. The final product provides an interesting alternative to chemical pesticides for Andean farmers affected by this potato pest.
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http://dx.doi.org/10.1016/j.jip.2012.11.014DOI Listing
February 2013

Exercise oxygen flow titration methods in COPD patients with respiratory failure.

Respir Med 2012 Nov 21;106(11):1544-50. Epub 2012 Jul 21.

Servicio de Neumología, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain.

We compare the adequacy of several titration procedures of oxygen flow in maintaining SpO(2) > 90% during the activities of daily life in patients with very severe COPD. Thirty-one very severe COPD patients undergoing oxygen-therapy were recruited. Three titration methods were randomly performed: (1) 6-min walking tests; (2) cycle-ergometer constant work-rate tests at a load equivalent to 12 ml/min/kg of oxygen uptake; (3) one single constant work-rate test at 40 W 12-h pulse-oximeter monitoring was performed on four consecutive days with the following oxygen flow during exercise: 1 l·min(-1) above the resting prescription (NOTT guidelines) and those established by the titration procedures. The time spent SpO(2) < 90% was higher for the titration based on NOTT and walking tests than for the oxygen flow established by the constant work-rate tests at 12 ml O(2)/min/kg (22.1 ± 18.7, 20.8 ± 19.5 and 6.7 ± 12.7%, respectively). As for the oxygen uptake-based titration, the simplified procedure (a single exercise test at 40 w) generates longer times spent SpO(2) < 90% and SpO(2) < 85%, although it maintains a SpO(2) > 90% for more 90% of the time. In COPD patients, exercise oxygen flow titrations by NOTT guidelines or walking tests do not allow a suitable oxygenation during the activities of daily life. Two more adequate alternative methods, based on constant work-rate tests, are proposed.
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http://dx.doi.org/10.1016/j.rmed.2012.06.021DOI Listing
November 2012

The effect of R249S carcinogenic and H168R-R249S suppressor mutations on p53-DNA interaction, a multi scale computational study.

Comput Biol Med 2010 May 18;40(5):498-508. Epub 2010 Apr 18.

Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai, Japan.

In this study we have undertaken the theoretical analysis of the effect of R249S carcinogenic and H168R-R249S suppressor mutation at core domain of the tumor suppressor protein p53, on its natural interaction with DNA using a newly developed method. The results show that the carcinogenic mutation R249S affects the flexibility of L3 loop region in p53, inducing the loss of important hydrogen bonds observed at interaction in the wild-type with DNA, on the other hand the suppressor mutation H168R on the R249S assists in maintaining the wild-type like flexibility of the L3 region in p53 and thus recover the interaction terms lost in the carcinogenic mutation alone. The present study sets a new direction in the development of new drugs that may restore the interactions that lost as a consequence of the carcinogenic mutations in p53.
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http://dx.doi.org/10.1016/j.compbiomed.2010.03.004DOI Listing
May 2010

Tribochemical reaction dynamics of molybdenum dithiocarbamate on nascent iron surface: a hybrid quantum chemical/classical molecular dynamics study.

J Nanosci Nanotechnol 2010 Apr;10(4):2495-502

Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, 6-6-11-1302 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.

Using a hybrid quantum chemical/classical molecular dynamics method, we have studied the tribochemical reaction dynamics of molybdenum dithiocarbamate (MoDTC), a commonly used friction modifier in automobile engine oils. MoDTC molecule adsorbed on rubbing nascent iron surface was situated. We firstly investigated the dynamic behavior of MoDTC molecule on the rubbing Fe(001) surface. During the friction simulation, the elongation of Mo-O bonds was observed, forming the Mo2S4 and thiocarbamic acid molecules. To unveil the detailed mechanism of this bond elongation, the electronic states of the MoDTC molecule and Fe(001) surface were computed, and the catalytic effects of Fe(001) surface to the molecule was found. We also found that extreme friction would influence the complete Mo-O bond dissociation. By using the hybrid quantum chemical/classical molecular dynamics method, we successfully simulated the tribochemical reaction dynamics of MoDTC as a friction modifier and obtained the influences of nascent iron surface and friction on its chemical reaction.
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http://dx.doi.org/10.1166/jnn.2010.1399DOI Listing
April 2010

Quantum chemistry study on absorption spectra, electronic and electrical properties of organic dye on anatase(001).

J Nanosci Nanotechnol 2010 Apr;10(4):2434-43

Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, 6-6-11-1302 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.

As the most reactive surface, the stoichiometric O-bridge terminated anatase(001) surface attracted considerable attentions in many application fields. The interfacial electron transfer in dye-sensitized anatase(001) plays a principal role in a variety of photoinduced reactions. In the present work, the UV-vis absorption spectrum of TiO2 bulk and different surface models were calculated by means of tight-binding quantum chemical molecular dynamics program "Colors-excite" for the first time. The thickness dependence on electronic and electrical properties of anatase(001) surface was achieved. The anatase(001) surface with a thickness of 1.0 nm shows excellent electronic and electrical properties. Moreover, the most suitable binding mode (dissociative adsorption) and absorption spectra of perylene with acrylic acid (PAA) on the optimum anatase(001) were investigated. A significant red-shift was observed from the UV-vis absorption spectrum of PAA/anatase(001) system. The red-shift occurring when PAA adsorbed on anatase(001) surface suggests that PAA/anatase(001) may be potential candidate for dye-sensitized solar cell. This study also proposed an effective computational tool "Colors-excite" to study of the electronic excitation properties for both molecular and periodic systems.
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http://dx.doi.org/10.1166/jnn.2010.1398DOI Listing
April 2010

A graph theoretical approach for assessing bio-macromolecular complex structural stability.

J Mol Model 2009 Nov 29;15(11):1349-70. Epub 2009 Apr 29.

Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Japan.

Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.
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http://dx.doi.org/10.1007/s00894-009-0494-1DOI Listing
November 2009
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