kevin Montes Silva - Academia.edu (original) (raw)
Papers by kevin Montes Silva
Applied Ocean Research
Critical evaluation and understanding of ship responses in the ocean is important for not only th... more Critical evaluation and understanding of ship responses in the ocean is important for not only the design and engineering of future platforms but also the operation and safety of those that are currently deployed. Simulations or experiments are typically performed in nominal sea conditions during ship design or prior to deployment, to evaluate different hullforms and develop operational profiles. Though it is necessary to analyze the response for nominal conditions, the results may not be reflective of the instantaneous state of the vessel and the ocean environment while deployed. Short-term temporal predictions of ship responses given the current wave environment and ship state would enable enhanced decision-making onboard and reduce the overall risk during operations for both manned and unmanned vessels, especially as the marine industry trends towards more autonomy. However, the current state-of-the-art in numerical hydrodynamic simulation tools are too computationally expensive to be employed for real-time ship motion forecasting and the computationally efficient tools are too low fidelity to provide accurate responses. Thus, a methodology is needed to provide fast and efficient predictions with levels of accuracy closer to the higher-fidelity tools.A methodology is developed with long short-term memory (LSTM) neural networks to represent the motions of a free running David Taylor Model Basin (DTMB) 5415 destroyer operating at 20 knots in Sea State 7 stern-quartering irregular seas. Case studies are performed for both course-keeping and turning circle scenarios. An estimate of the vessel's encounter frame is made with the trajectories observed in the training dataset. Wave elevation time histories are given by artificial wave probes that travel with the estimated encounter frame and serve as input into the neural network, while the output is the 6-DOF temporal ship motion response. Overall, the neural network is able to predict the temporal response of the ship due to unseen waves accurately, which makes this methodology suitable for system identification and real-time ship motion forecasting. The methodology, the dependence of model accuracy on wave probe and training data quantity and the estimated encounter frame are all detailed.
The 9th Conference on Computational Methods in Marine Engineering (Marine 2021)
Accurate and efficient prediction of extreme ship responses continues to be an important and chal... more Accurate and efficient prediction of extreme ship responses continues to be an important and challenging problem in ship hydrodynamics. Probabilistic frameworks in conjunction with computationally efficient numerical hydrodynamic tools such as volume-based and potential flow methods have been developed that allow researchers and ship designers to better understand extreme events. However, the ability of these tools to represent the physics quantitatively during extreme events is limited and not robust to different problems. Therefore, model testing will continue to be important in analysis, and more emphasis will be placed on high fidelity computational fluid dynamics (CFD) simulations. Experiments and CFD both come at well documented costs and require a systematic approach to target extreme events. The critical wave groups method (CWG) has been implemented with CFD, and the integration of high fidelity simulations with extreme event probabilistic methods has been previously showcased. The implementation of CWG with CFD is achieved by embedding deterministic wave groups into previously run irregular wave trains such that the motion state of the ship at the moment of encountering the wave group is known. Embedding the deterministic wave groups into an irregular wave train results in a composite wave train that can be evaluated with numerical hydrodynamic simulation tools such as CFD, or even a model test. Though the CWG method does allow for less simulation time than a Monte Carlo type approach, the large number of runs required may still be cost-prohibitive. The objective of the present work is to develop an approach where a limited set of expensive simulations or experiments build a time-accurate long short-term memory (LSTM) neural network model that rapidly identifies critical wave groups that lead to a response exceeding a specified threshold. This paper compares the LSTM modeling approach of building a single neural network for all wave groups to establishing an ensemble of neural networks, each responsible for wave groups with specific parameters. The ensemble approach showcases better accuracy, a higher convergence with respect to data quantity, and produces responses that are representative of the CFD simulations.
Abstract : The static response of a circular cylindrical open shell (curved panel) constructed of... more Abstract : The static response of a circular cylindrical open shell (curved panel) constructed of an orthotropic graphite/epoxy laminate is numerically investigated in this thesis. The shell is subjected to an inward point load, centered on and normal to the shell surface, which maintains its original orientation through deformation (i.e. dead load). The shell displacement response is seen to vary widely with shell geometry and boundary conditions, not only in magnitude of deformation but also in the nature and progression of the collapse under critical load. The finite element analysis is conducted with a quasi-two dimensional thin shell element which incorporates parabolic transverse shear stress through the thickness. The element can be formulated with either large displacement/rotation kinematics or the simpler Donnell relations. To enable tracking through critical load and displacement points and investigation of the post-critical regime, a solution algorithm other than the popular Newton- Raphson technique with displacement control or load control is required. The algorithm employed here uses a modified Riks/Wempner technique. It allows continuous tracing of the load - deflection response through critical load and critical displacement points. Step size is automatically scaled to follow the solution path closely in the areas of large load or displacement changes which surround critical points. (KR)
SILVA, KEVIN J., M.S., August 2013, Athletic Training Validation of the Movement Activity in Phys... more SILVA, KEVIN J., M.S., August 2013, Athletic Training Validation of the Movement Activity in Physical Space System as a Functional Outcome Measure Following Anterior Cruciate Ligament Reconstruction Surgery Director of Thesis: Brian G. Ragan Introduction: The World Health Organization’s International Classification of Functioning, Disability, and Health (WHO ICF) defines function as the interaction between body function and activity within the social environment. Current outcome measures fail to assess physical activity within free-living environments. Measuring physical activity within free-living environments may be a more accurate measure of function. The Movement and Activity in Physical Space (MAPS) System has been developed and validated as an objective functional outcome measure that combines physical activity data with free-living environmental interactions. An accelerometer records acceleration and steps and global positioning system (GPS) device measures environmental interactions. These data are then combined to produce raw scores that represent function using the MAPS formula. Purpose: The primary purpose of this study was to further develop and validate the MAPS system as an objective functional outcome measure following anterior cruciate ligament (ACL) reconstruction surgery. The secondary purpose of this study was to determine if MAPS scores are sensitive to change throughout the recovery process. Methods: An observational and longitudinal study was designed. A total of 8 participants completed 4 data collection sessions following ACL surgery (n = 8, mean ± SD; age, 19.71 ± 1.98y; height, 177.44 ± 6.12cm; weight, 83.12 ± 4 12.44kg). Physical activity data (accelerometer) and geospatial locations (GPS) were analyzed for each day of data collection. Results: Person product correlation showed little to no correlation between the KOOS and PROMIS assessments when compared to MAPS scores. MAPSAC and MAPSS scores observed a 445% and 513% percent change from SI + 1-10 and SI + 36-40, respectively. Dependent t-test comparing SI + 1-10 to SI + 36-40 showed that the MAPS scores were statistically different over time. Conclusion: The MAPS System has been developed to measure physical activity within the free-living environmental as the main components of function. The results of this study provide validity evidence for both MAPS acceleration (MAPSAC) and MAPS steps (MAPSS) scores to detect progression or regression following ACL reconstruction surgery. Further research and development of the MAPS System is needed to observe other populations.
Background: Hand hygiene (HH) is a primary measure to prevent spread of acute respiratory infecti... more Background: Hand hygiene (HH) is a primary measure to prevent spread of acute respiratory infections (ARI); however, performance frequency among healthcare personnel (HCP) is often less than optimal. During the ARI season, HCP education focuses on enhanced need for HH and respiratory protection. A mild (2011-12) and moderately severe (2012-13) ARI season are compared to observe if increased ARI incidence results in greater HH performance in outpatient clinics with high exposure to ARI. Methods: To determine if study week, season, or ARI incidence drives compliance, HH observers collected compliance from HCPs participating in the Respiratory Protection Effectiveness Clinical Trial during the 2011-12 (YR1) and 2012-13 (YR2) respiratory seasons. Within 3 geographically diverse medical centers (CO, MD, NY), WHO's 5 Moments HH compliance data was collected over 12 weeks each season. Regional CDC influenza surveillance data (Regions 2, 3, & 8) determined season severity. Linear regres...
Background: Acute Respiratory Illnesses (ARIs) are transmissible between patients and Healthcare ... more Background: Acute Respiratory Illnesses (ARIs) are transmissible between patients and Healthcare Personnel (HCPs) in outpatient clinics. HCPs are at an elevated exposure risk when interacting with patient with ARI symptoms. To test the hypothesis that HCPs who perform respiratory procedures on ARI patients are at a greater risk of developing ARI symptoms when compared to their counterparts, we investigated HCP self-reported symptomatic days (sick days) as a means to provide insight to exposure risk. Methods : Daily work shift survey data was collected from HCPs at 7 sites across the country for 12 weeks during the peak of the 2012-2013 influenza season as part of the Respiratory Protection Effectiveness Clinical Trial (ResPECT). HCPs reported ARI patient contact, type and frequency of respiratory procedures performed (Intubation, Airway Suction, Nebulizer, Nasopharyngeal Aspiration), and self-reported respiratory symptomatic days. For this analysis, HCPs were assigned to either the ...
The Journal of Foraminiferal Research, 1996
Analysis of Rose Bengal-stained benthic foraminifera from six box cores collected from the San Pe... more Analysis of Rose Bengal-stained benthic foraminifera from six box cores collected from the San Pedro Basin in April, July, and October, 1988 (-720 m water depth) reveals that the foraminiferal assemblages vary during this six month period. Species diversity is low, with five to six species constituting 90% of the total abundance in the >150 p m fraction. In the 63-150 p m fraction, eight species account for 90% of the total abundance in April, decreasing to three species in July, and increasing to seven in October. Species are vertically stratified within the sediments, reflecting microhabitat preferences, and are grouped according to their vertical patterns. In the >150 p m fraction, three groups occur: 1) taxa having maxima from 0-1 em, 2) infaunal taxa with maxima from 1.5-3 cm, and 3) species with more complex distributions. In the 63-150 p m fraction, two groups are identified: 1) infaunal species having maxima between 1-6 cm, and 2) species with variable distributions in April, nearly absent in July, and displaying subsurface maxima in October. No change in species distribution patterns was observed between April and October in either size fraction. A comparison of the two size fractions of Chilostomella ovoidea and Buliminella tenuata shows similar depth profiles, which suggests that there are no ontogenetic changes of microhabitat preferences of these two taxa. Maxima of Nonionelln stelln and Buliminella tenuafa in July and Bolivina spissa, Chilostomella ovoidea, Globobulimina pacifica, Fursenkoina bramlettei, and the agglutinated foraminifera in October suggest that rapid growth occurred over a three month period.
Developmental Biology, 2012
Zygote arrest (Zar) proteins are crucial for early embryonic development, but their molecular mec... more Zygote arrest (Zar) proteins are crucial for early embryonic development, but their molecular mechanism of action is unknown. The Translational Control Sequence (TCS) in the 3 0 untranslated region (UTR) of the maternal mRNA, Wee1, mediates translational repression in immature Xenopus oocytes and translational activation in mature oocytes, but the protein that binds to the TCS and mediates translational control is not known. Here we show that Xenopus laevis Zar2 (encoded by zar2) binds to the TCS in maternal Wee1 mRNA and represses translation in immature oocytes. Using yeast 3 hybrid assays and electrophoretic mobility shift assays, Zar2 was shown to bind specifically to the TCS in the Wee1 3 0 UTR. RNA binding required the presence of Zn 2 þ and conserved cysteines in the C-terminal domain, suggesting that Zar2 contains a zinc finger. Consistent with regulating maternal mRNAs, Zar2 was present throughout oogenesis, and endogenous Zar2 co-immunoprecipitated endogenous Wee1 mRNA from immature oocytes, demonstrating the physiological significance of the protein-RNA interaction. Interestingly, Zar2 levels decreased during oocyte maturation. Dual luciferase reporter tethered assays showed that Zar2 repressed translation in immature oocytes. Translational repression was relieved during oocyte maturation and this coincided with degradation of Zar2 during maturation. This is the first report of a molecular function of zygote arrest proteins. These data show that Zar2 contains a zinc finger and is a transacting factor for the TCS in maternal mRNAs in immature Xenopus oocytes.
Developmental Biology, 2011
Hedgehog (Hh) signaling controls gene transcription through the Gli family of transcription facto... more Hedgehog (Hh) signaling controls gene transcription through the Gli family of transcription factors, including Drosophila Ci. In the absence of Hh, Ci acts as a transcriptional repressor, but upon signaling activation, Ci becomes a transcriptional activator. Two Hh target genes, patched (ptc) and decapentaplegic (dpp) contain enhancers with Ci binding sites. The ptc enhancer has three highaffinity Ci sites, whereas the dpp enhancer has only low-affinity sites. In the developing wing, ptc is expressed in a narrow stripe of cells that receive the highest levels of Hh, while dpp is expressed in a broader stripe in a region of moderate signaling. We found that dpp requires low-affinity sites for optimal activation by Hh, as replacing the low-affinity binding sites of dpp with high-affinity sites from ptc caused repression of dpp in cells that receive moderate signaling. Because higher binding affinity correlates with increased Ci occupancy of these enhancers, our results are consistent with the idea that Ci may act more cooperatively as a repressor than as an activator in cells that have both forms of this transcription factor. To test this hypothesis, we quantified the expression of synthetic enhancers with three high-affinity sites versus one high-affinity site. Our data showed that having a single high-affinity site abolishes the transcriptional repression observed in enhancers with multiple high-affinity sites. These results are consistent with the cooperative repression model, thus we propose a novel transcriptional mechanism to interpret the Hh signaling gradient.
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2013
Maternal mRNAs are translationally regulated during early development. Zar1 and its closely relat... more Maternal mRNAs are translationally regulated during early development. Zar1 and its closely related homolog, Zar2, are both crucial in early development. Xenopus laevis Zygote arrest 2 (Zar2) binds to the Translational Control Sequence (TCS) in maternal mRNAs and regulates translation. The molecular mechanism of Zar1 has not been described. Here we report similarities and differences between Xenopus Zar1 and Zar2. Analysis of Zar sequences in vertebrates revealed two Zar family members with conserved, characteristic amino acid differences in the Cterminal domain. The presence of only two vertebrate Zar proteins was supported by analyzing Zar1 synteny. We propose that the criteria for naming Zar sequences are based on the characteristic amino acids and the chromosomal context. We also propose reclassification of some Zar sequences. We found that Zar1 is expressed throughout oogenesis and is stable during oocyte maturation. The N-terminal domain of Zar1 repressed translation of a reporter construct in immature oocytes. Both Zar1 and Zar2 bound to the TCS in the Wee1 and Mos 3 UTRs using a zinc finger in the C-terminal domain. However, Zar1 had much higher affinity for RNA than Zar2. To show the functional significance of the conserved amino acid substitutions, these residues in Zar2 were mutated to those found in Zar1. We show that these residues contributed to the different RNA binding characteristics of Zar1 compared to Zar2. Our study shows that Zar proteins have generally similar molecular functions in the translational regulation of maternal mRNAs, but they may have different roles in early development.
Foods, 2021
Cv. Arbequina extra virgin olive oils (EVOO) were flavored with cinnamon, garlic, and rosemary an... more Cv. Arbequina extra virgin olive oils (EVOO) were flavored with cinnamon, garlic, and rosemary and characterized. Although flavoring significantly affected the physicochemical quality parameters, all oils fulfilled the legal thresholds for EVOO classification. Flavoring increased (20 to 40%) the total phenolic contents, whereas oxidative stability was dependent on the flavoring agent (a slight increase for rosemary and a decrease for cinnamon and garlic). Flavoring also had a significant impact on the sensory profiles. Unflavored oils, cinnamon, and garlic flavored oils had a fruity-ripe sensation while rosemary flavored oils were fruity-green oils. Fruit-related sensations, perceived in unflavored oils, disappeared with flavoring. Flavoring decreased the sweetness, enhanced the bitterness, and did not influence the pungency of the oils. According to the EU regulations, flavored oils cannot be commercialized as EVOO. Thus, to guarantee the legal labelling requirement and to meet the...
Applied Ocean Research
Critical evaluation and understanding of ship responses in the ocean is important for not only th... more Critical evaluation and understanding of ship responses in the ocean is important for not only the design and engineering of future platforms but also the operation and safety of those that are currently deployed. Simulations or experiments are typically performed in nominal sea conditions during ship design or prior to deployment, to evaluate different hullforms and develop operational profiles. Though it is necessary to analyze the response for nominal conditions, the results may not be reflective of the instantaneous state of the vessel and the ocean environment while deployed. Short-term temporal predictions of ship responses given the current wave environment and ship state would enable enhanced decision-making onboard and reduce the overall risk during operations for both manned and unmanned vessels, especially as the marine industry trends towards more autonomy. However, the current state-of-the-art in numerical hydrodynamic simulation tools are too computationally expensive to be employed for real-time ship motion forecasting and the computationally efficient tools are too low fidelity to provide accurate responses. Thus, a methodology is needed to provide fast and efficient predictions with levels of accuracy closer to the higher-fidelity tools.A methodology is developed with long short-term memory (LSTM) neural networks to represent the motions of a free running David Taylor Model Basin (DTMB) 5415 destroyer operating at 20 knots in Sea State 7 stern-quartering irregular seas. Case studies are performed for both course-keeping and turning circle scenarios. An estimate of the vessel's encounter frame is made with the trajectories observed in the training dataset. Wave elevation time histories are given by artificial wave probes that travel with the estimated encounter frame and serve as input into the neural network, while the output is the 6-DOF temporal ship motion response. Overall, the neural network is able to predict the temporal response of the ship due to unseen waves accurately, which makes this methodology suitable for system identification and real-time ship motion forecasting. The methodology, the dependence of model accuracy on wave probe and training data quantity and the estimated encounter frame are all detailed.
The 9th Conference on Computational Methods in Marine Engineering (Marine 2021)
Accurate and efficient prediction of extreme ship responses continues to be an important and chal... more Accurate and efficient prediction of extreme ship responses continues to be an important and challenging problem in ship hydrodynamics. Probabilistic frameworks in conjunction with computationally efficient numerical hydrodynamic tools such as volume-based and potential flow methods have been developed that allow researchers and ship designers to better understand extreme events. However, the ability of these tools to represent the physics quantitatively during extreme events is limited and not robust to different problems. Therefore, model testing will continue to be important in analysis, and more emphasis will be placed on high fidelity computational fluid dynamics (CFD) simulations. Experiments and CFD both come at well documented costs and require a systematic approach to target extreme events. The critical wave groups method (CWG) has been implemented with CFD, and the integration of high fidelity simulations with extreme event probabilistic methods has been previously showcased. The implementation of CWG with CFD is achieved by embedding deterministic wave groups into previously run irregular wave trains such that the motion state of the ship at the moment of encountering the wave group is known. Embedding the deterministic wave groups into an irregular wave train results in a composite wave train that can be evaluated with numerical hydrodynamic simulation tools such as CFD, or even a model test. Though the CWG method does allow for less simulation time than a Monte Carlo type approach, the large number of runs required may still be cost-prohibitive. The objective of the present work is to develop an approach where a limited set of expensive simulations or experiments build a time-accurate long short-term memory (LSTM) neural network model that rapidly identifies critical wave groups that lead to a response exceeding a specified threshold. This paper compares the LSTM modeling approach of building a single neural network for all wave groups to establishing an ensemble of neural networks, each responsible for wave groups with specific parameters. The ensemble approach showcases better accuracy, a higher convergence with respect to data quantity, and produces responses that are representative of the CFD simulations.
Abstract : The static response of a circular cylindrical open shell (curved panel) constructed of... more Abstract : The static response of a circular cylindrical open shell (curved panel) constructed of an orthotropic graphite/epoxy laminate is numerically investigated in this thesis. The shell is subjected to an inward point load, centered on and normal to the shell surface, which maintains its original orientation through deformation (i.e. dead load). The shell displacement response is seen to vary widely with shell geometry and boundary conditions, not only in magnitude of deformation but also in the nature and progression of the collapse under critical load. The finite element analysis is conducted with a quasi-two dimensional thin shell element which incorporates parabolic transverse shear stress through the thickness. The element can be formulated with either large displacement/rotation kinematics or the simpler Donnell relations. To enable tracking through critical load and displacement points and investigation of the post-critical regime, a solution algorithm other than the popular Newton- Raphson technique with displacement control or load control is required. The algorithm employed here uses a modified Riks/Wempner technique. It allows continuous tracing of the load - deflection response through critical load and critical displacement points. Step size is automatically scaled to follow the solution path closely in the areas of large load or displacement changes which surround critical points. (KR)
SILVA, KEVIN J., M.S., August 2013, Athletic Training Validation of the Movement Activity in Phys... more SILVA, KEVIN J., M.S., August 2013, Athletic Training Validation of the Movement Activity in Physical Space System as a Functional Outcome Measure Following Anterior Cruciate Ligament Reconstruction Surgery Director of Thesis: Brian G. Ragan Introduction: The World Health Organization’s International Classification of Functioning, Disability, and Health (WHO ICF) defines function as the interaction between body function and activity within the social environment. Current outcome measures fail to assess physical activity within free-living environments. Measuring physical activity within free-living environments may be a more accurate measure of function. The Movement and Activity in Physical Space (MAPS) System has been developed and validated as an objective functional outcome measure that combines physical activity data with free-living environmental interactions. An accelerometer records acceleration and steps and global positioning system (GPS) device measures environmental interactions. These data are then combined to produce raw scores that represent function using the MAPS formula. Purpose: The primary purpose of this study was to further develop and validate the MAPS system as an objective functional outcome measure following anterior cruciate ligament (ACL) reconstruction surgery. The secondary purpose of this study was to determine if MAPS scores are sensitive to change throughout the recovery process. Methods: An observational and longitudinal study was designed. A total of 8 participants completed 4 data collection sessions following ACL surgery (n = 8, mean ± SD; age, 19.71 ± 1.98y; height, 177.44 ± 6.12cm; weight, 83.12 ± 4 12.44kg). Physical activity data (accelerometer) and geospatial locations (GPS) were analyzed for each day of data collection. Results: Person product correlation showed little to no correlation between the KOOS and PROMIS assessments when compared to MAPS scores. MAPSAC and MAPSS scores observed a 445% and 513% percent change from SI + 1-10 and SI + 36-40, respectively. Dependent t-test comparing SI + 1-10 to SI + 36-40 showed that the MAPS scores were statistically different over time. Conclusion: The MAPS System has been developed to measure physical activity within the free-living environmental as the main components of function. The results of this study provide validity evidence for both MAPS acceleration (MAPSAC) and MAPS steps (MAPSS) scores to detect progression or regression following ACL reconstruction surgery. Further research and development of the MAPS System is needed to observe other populations.
Background: Hand hygiene (HH) is a primary measure to prevent spread of acute respiratory infecti... more Background: Hand hygiene (HH) is a primary measure to prevent spread of acute respiratory infections (ARI); however, performance frequency among healthcare personnel (HCP) is often less than optimal. During the ARI season, HCP education focuses on enhanced need for HH and respiratory protection. A mild (2011-12) and moderately severe (2012-13) ARI season are compared to observe if increased ARI incidence results in greater HH performance in outpatient clinics with high exposure to ARI. Methods: To determine if study week, season, or ARI incidence drives compliance, HH observers collected compliance from HCPs participating in the Respiratory Protection Effectiveness Clinical Trial during the 2011-12 (YR1) and 2012-13 (YR2) respiratory seasons. Within 3 geographically diverse medical centers (CO, MD, NY), WHO's 5 Moments HH compliance data was collected over 12 weeks each season. Regional CDC influenza surveillance data (Regions 2, 3, & 8) determined season severity. Linear regres...
Background: Acute Respiratory Illnesses (ARIs) are transmissible between patients and Healthcare ... more Background: Acute Respiratory Illnesses (ARIs) are transmissible between patients and Healthcare Personnel (HCPs) in outpatient clinics. HCPs are at an elevated exposure risk when interacting with patient with ARI symptoms. To test the hypothesis that HCPs who perform respiratory procedures on ARI patients are at a greater risk of developing ARI symptoms when compared to their counterparts, we investigated HCP self-reported symptomatic days (sick days) as a means to provide insight to exposure risk. Methods : Daily work shift survey data was collected from HCPs at 7 sites across the country for 12 weeks during the peak of the 2012-2013 influenza season as part of the Respiratory Protection Effectiveness Clinical Trial (ResPECT). HCPs reported ARI patient contact, type and frequency of respiratory procedures performed (Intubation, Airway Suction, Nebulizer, Nasopharyngeal Aspiration), and self-reported respiratory symptomatic days. For this analysis, HCPs were assigned to either the ...
The Journal of Foraminiferal Research, 1996
Analysis of Rose Bengal-stained benthic foraminifera from six box cores collected from the San Pe... more Analysis of Rose Bengal-stained benthic foraminifera from six box cores collected from the San Pedro Basin in April, July, and October, 1988 (-720 m water depth) reveals that the foraminiferal assemblages vary during this six month period. Species diversity is low, with five to six species constituting 90% of the total abundance in the >150 p m fraction. In the 63-150 p m fraction, eight species account for 90% of the total abundance in April, decreasing to three species in July, and increasing to seven in October. Species are vertically stratified within the sediments, reflecting microhabitat preferences, and are grouped according to their vertical patterns. In the >150 p m fraction, three groups occur: 1) taxa having maxima from 0-1 em, 2) infaunal taxa with maxima from 1.5-3 cm, and 3) species with more complex distributions. In the 63-150 p m fraction, two groups are identified: 1) infaunal species having maxima between 1-6 cm, and 2) species with variable distributions in April, nearly absent in July, and displaying subsurface maxima in October. No change in species distribution patterns was observed between April and October in either size fraction. A comparison of the two size fractions of Chilostomella ovoidea and Buliminella tenuata shows similar depth profiles, which suggests that there are no ontogenetic changes of microhabitat preferences of these two taxa. Maxima of Nonionelln stelln and Buliminella tenuafa in July and Bolivina spissa, Chilostomella ovoidea, Globobulimina pacifica, Fursenkoina bramlettei, and the agglutinated foraminifera in October suggest that rapid growth occurred over a three month period.
Developmental Biology, 2012
Zygote arrest (Zar) proteins are crucial for early embryonic development, but their molecular mec... more Zygote arrest (Zar) proteins are crucial for early embryonic development, but their molecular mechanism of action is unknown. The Translational Control Sequence (TCS) in the 3 0 untranslated region (UTR) of the maternal mRNA, Wee1, mediates translational repression in immature Xenopus oocytes and translational activation in mature oocytes, but the protein that binds to the TCS and mediates translational control is not known. Here we show that Xenopus laevis Zar2 (encoded by zar2) binds to the TCS in maternal Wee1 mRNA and represses translation in immature oocytes. Using yeast 3 hybrid assays and electrophoretic mobility shift assays, Zar2 was shown to bind specifically to the TCS in the Wee1 3 0 UTR. RNA binding required the presence of Zn 2 þ and conserved cysteines in the C-terminal domain, suggesting that Zar2 contains a zinc finger. Consistent with regulating maternal mRNAs, Zar2 was present throughout oogenesis, and endogenous Zar2 co-immunoprecipitated endogenous Wee1 mRNA from immature oocytes, demonstrating the physiological significance of the protein-RNA interaction. Interestingly, Zar2 levels decreased during oocyte maturation. Dual luciferase reporter tethered assays showed that Zar2 repressed translation in immature oocytes. Translational repression was relieved during oocyte maturation and this coincided with degradation of Zar2 during maturation. This is the first report of a molecular function of zygote arrest proteins. These data show that Zar2 contains a zinc finger and is a transacting factor for the TCS in maternal mRNAs in immature Xenopus oocytes.
Developmental Biology, 2011
Hedgehog (Hh) signaling controls gene transcription through the Gli family of transcription facto... more Hedgehog (Hh) signaling controls gene transcription through the Gli family of transcription factors, including Drosophila Ci. In the absence of Hh, Ci acts as a transcriptional repressor, but upon signaling activation, Ci becomes a transcriptional activator. Two Hh target genes, patched (ptc) and decapentaplegic (dpp) contain enhancers with Ci binding sites. The ptc enhancer has three highaffinity Ci sites, whereas the dpp enhancer has only low-affinity sites. In the developing wing, ptc is expressed in a narrow stripe of cells that receive the highest levels of Hh, while dpp is expressed in a broader stripe in a region of moderate signaling. We found that dpp requires low-affinity sites for optimal activation by Hh, as replacing the low-affinity binding sites of dpp with high-affinity sites from ptc caused repression of dpp in cells that receive moderate signaling. Because higher binding affinity correlates with increased Ci occupancy of these enhancers, our results are consistent with the idea that Ci may act more cooperatively as a repressor than as an activator in cells that have both forms of this transcription factor. To test this hypothesis, we quantified the expression of synthetic enhancers with three high-affinity sites versus one high-affinity site. Our data showed that having a single high-affinity site abolishes the transcriptional repression observed in enhancers with multiple high-affinity sites. These results are consistent with the cooperative repression model, thus we propose a novel transcriptional mechanism to interpret the Hh signaling gradient.
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2013
Maternal mRNAs are translationally regulated during early development. Zar1 and its closely relat... more Maternal mRNAs are translationally regulated during early development. Zar1 and its closely related homolog, Zar2, are both crucial in early development. Xenopus laevis Zygote arrest 2 (Zar2) binds to the Translational Control Sequence (TCS) in maternal mRNAs and regulates translation. The molecular mechanism of Zar1 has not been described. Here we report similarities and differences between Xenopus Zar1 and Zar2. Analysis of Zar sequences in vertebrates revealed two Zar family members with conserved, characteristic amino acid differences in the Cterminal domain. The presence of only two vertebrate Zar proteins was supported by analyzing Zar1 synteny. We propose that the criteria for naming Zar sequences are based on the characteristic amino acids and the chromosomal context. We also propose reclassification of some Zar sequences. We found that Zar1 is expressed throughout oogenesis and is stable during oocyte maturation. The N-terminal domain of Zar1 repressed translation of a reporter construct in immature oocytes. Both Zar1 and Zar2 bound to the TCS in the Wee1 and Mos 3 UTRs using a zinc finger in the C-terminal domain. However, Zar1 had much higher affinity for RNA than Zar2. To show the functional significance of the conserved amino acid substitutions, these residues in Zar2 were mutated to those found in Zar1. We show that these residues contributed to the different RNA binding characteristics of Zar1 compared to Zar2. Our study shows that Zar proteins have generally similar molecular functions in the translational regulation of maternal mRNAs, but they may have different roles in early development.
Foods, 2021
Cv. Arbequina extra virgin olive oils (EVOO) were flavored with cinnamon, garlic, and rosemary an... more Cv. Arbequina extra virgin olive oils (EVOO) were flavored with cinnamon, garlic, and rosemary and characterized. Although flavoring significantly affected the physicochemical quality parameters, all oils fulfilled the legal thresholds for EVOO classification. Flavoring increased (20 to 40%) the total phenolic contents, whereas oxidative stability was dependent on the flavoring agent (a slight increase for rosemary and a decrease for cinnamon and garlic). Flavoring also had a significant impact on the sensory profiles. Unflavored oils, cinnamon, and garlic flavored oils had a fruity-ripe sensation while rosemary flavored oils were fruity-green oils. Fruit-related sensations, perceived in unflavored oils, disappeared with flavoring. Flavoring decreased the sweetness, enhanced the bitterness, and did not influence the pungency of the oils. According to the EU regulations, flavored oils cannot be commercialized as EVOO. Thus, to guarantee the legal labelling requirement and to meet the...