ImportanceOphthalmology-residency selection committees require robust metrics to review applicant... more ImportanceOphthalmology-residency selection committees require robust metrics to review applicants. Participation in research activities is a core component of the application process for its perceived association with future academic productivity.ObjectiveTo evaluate the correlation between the number of preresidency peer-reviewed publications (PPPs) and subsequent peer-reviewed publications or career choices of ophthalmology residency graduates.Design, Setting, and ParticipantsIn this cross-sectional study, names of ophthalmology residency graduates were obtained. PubMed-indexed publication records were generated and publications were categorized as preresidency, intraresidency, and postresidency. First author and journal publications with an impact factor (IF) score of 3 or more were recorded. Current academic and community-based career statuses were designated. Names were obtained from cohort and alumni lists on residency program websites or by emailing program directors. Partic...
Purpose of Review In this article, we reviewed the impact resulting from the COVID-19 pandemic on... more Purpose of Review In this article, we reviewed the impact resulting from the COVID-19 pandemic on the traditional model of care in ophthalmology. Recent Findings Though virtual eye care has been present for more than 20 years, the COVID-19 pandemic has established a precedent to seriously consider its role in the evolving paradigm of vision and eye care. New hybrid models of care have enhanced or replaced traditional synchronous and asynchronous visits. The increased use of smart phoneography and mobile applications enhanced the remote examination of patients. Use of e-learning became a mainstream tool to continue accessing education and training. Summary Teleophthalmology has demonstrated its value for screening, examining, diagnosing, monitoring treatment, and increasing access to education. However, much of the progress made following the COVID-19 pandemic is at risk of being lost as society pushes to reestablish normalcy. Further studies during the new norm are required to prove a more permanent role for virtual eye care.
<p>(a) TD game: individuals make higher claims when the reward/punishment parameter is low,... more <p>(a) TD game: individuals make higher claims when the reward/punishment parameter is low, and make lower claims when is high. (b) MEC game: individuals expend more effort when the effort cost is low, and less effort when is high.</p
<p>(a)(c)(d)(e)(f) Average effort levels in the smoothed MEC game over the last of generati... more <p>(a)(c)(d)(e)(f) Average effort levels in the smoothed MEC game over the last of generations versus the effort cost parameter for different values of the smoothing parameter , on a complete graph (a), a random regular graph with degree 10 (c), a scale-free graph with mean degree 10 (d), 2D lattice graph with 4 neighbors (e), and 2D lattice graph with 8 neighbors (f). Parameter values: for lattice graphs and for other graphs, , and . (b) Number of individuals versus their effort levels , when and , on a complete graph with parameter values: , and .</p
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of micr... more Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function Users may view, print, copy, and download text and data-mine the content in such documents, for the...
effect of vibrotactile feedback on postural sway during locomotor activities (Article begins on n... more effect of vibrotactile feedback on postural sway during locomotor activities (Article begins on next page) The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters.
Purpose To describe the relationship between the number of Federal Drug Administration (FDA)-appr... more Purpose To describe the relationship between the number of Federal Drug Administration (FDA)-approved manufacturers and the price change of generic and branded topical eye drops. Methods Retrospective analysis of topical eye drop medications with formulations listed in the FDA Orange Book and the National Average Drug Acquisition Cost database from 2013 to 2017. Results The most frequently prescribed generic topical drugs were glaucoma medications (34%), antimicrobials (32%), anti-inflammatories (24%), mydriatics (5%), and anesthetics (5%). The most frequently prescribed branded topical drugs were anti-inflammatories (45%), glaucoma medications (32%), antimicrobials (21%) and dry eye medications (3%). From 2013 to 2017, generic eye drops had a median price decrease of 20% (IQR 32%) while branded eye drops had a median price increase of 44% (IQR 28%) (P < .001). A significant inverse association was identified between the price change of generic eye drops and the total number of a...
Cyanobacteria have multifaceted ecological roles on coral reefs. Moorena bouillonii, a chemically... more Cyanobacteria have multifaceted ecological roles on coral reefs. Moorena bouillonii, a chemically rich filamentous cyanobacterium, has been characterized as a pathogenic organism with an unusual ability to overgrow gorgonian corals, but little has been done to study its general growth habits or its unique association with the snapping shrimp Alpheus frontalis. Quantitative benthic surveys, and field and photographic observations were utilized to develop a better understanding of the ecology of these species, while growth experiments and nutrient analysis were performed to examine how this cyanobacterium may be benefiting from its shrimp symbiont. Colonies of M. bouillonii and A. frontalis displayed considerable habitat specificity in terms of occupied substrate. Although found to vary in abundance and density across survey sites and transects, M. bouillonii was consistently found to be thriving with A. frontalis within interstitial spaces on the reef. Removal of A. frontalis from cy...
OBJECTIVES: To determine the incidence of refeeding syndrome in otherwise healthy children <3 ... more OBJECTIVES: To determine the incidence of refeeding syndrome in otherwise healthy children <3 years of age admitted for failure to thrive (FTT). METHODS: A multicenter retrospective cohort study was performed on patients aged ≤36 months admitted with a primary diagnosis of FTT from January 1, 2011, to December 31, 2016. The primary outcome measure was the percentage of patients with laboratory evidence of refeeding syndrome. Exclusion criteria included admission to an ICU, parenteral nutrition, history of prematurity, gastrostomy tube feeds, and any complex chronic conditions. RESULTS: Of the 179 patients meeting inclusion criteria, none had laboratory evidence of refeeding syndrome. Of these, 145 (81%) had laboratory work done at the time of admission, and 69 (39%) had laboratory work repeated after admission. A small percentage (6%) of included patients experienced an adverse event due to repeat laboratory draw. CONCLUSIONS: In otherwise healthy hospitalized patients <3 year...
The tropical marine cyanobacterium Moorena bouillonii occupies a large geographic range across th... more The tropical marine cyanobacterium Moorena bouillonii occupies a large geographic range across the Indian and Western Tropical Pacific Oceans and is a prolific producer of structurally unique and biologically active natural products. An ensemble of computational approaches, including the creation of the ORCA (Objective Relational Comparative Analysis) pipeline for flexible MS1 feature detection and multivariate analyses, were used to analyze various M. bouillonii samples. The observed chemogeographic patterns suggested the production of regionally specific natural products by M. bouillonii. Analyzing the drivers of these chemogeographic patterns allowed for the identification, targeted isolation, and structure elucidation of a regionally specific natural product, doscadenamide A (1). Analyses of MS2 fragmentation patterns further revealed this natural product to be part of an extensive family of herein annotated, proposed natural structural analogs (doscadenamides B–J, 2–10); the en...
IOP Conference Series: Materials Science and Engineering, 2020
Philippines lie in the Pacific Ring of Fire, a region where earthquakes and other seismic activit... more Philippines lie in the Pacific Ring of Fire, a region where earthquakes and other seismic activities are frequent. Through the NBCDO Memorandum Circular No. 01 Series of 2015, The DPWH Guidelines and Implementing Rules on Earthquake Recording Instrumentation for buildings was implemented with the objectives of: (1) ensuring the safety of building occupants by determining the condition of buildings, and (2) collecting earthquake related data during major seismic activities. Despite being signed on March 12, 2015, the compliance rate of the buildings here in the City of Manila was low. The purpose of this study is to determine the cost impact of the said guidelines to building owners using MCDA-AHP; as well as to identify the amount needed to equip the City of Manila. The research was carried out having SHM experts (for AHP) and building owners (for MCDA) as the respondents for the corresponding parts of the study. The results show that the equipment price has the biggest impact to the building owners and their willingness to pay for ERIs is lower compared to the market.
BACKGROUND: Magnetic resonance-guided laser-interstitial thermotherapy (MR-LITT) is a minimally i... more BACKGROUND: Magnetic resonance-guided laser-interstitial thermotherapy (MR-LITT) is a minimally invasive technique that shows promise in neuro-oncology because of its superiority in delivering precise minimally invasive thermal energy with minimal collateral damage. OBJECTIVE: In this analysis, we investigate initial data on the use of MR-LITT in the treatment of newly diagnosed high-grade gliomas. METHODS: With the use of the PubMed, OVID, and Google-scholar database systems, a comprehensive search of the English literature was performed. Eighty-five articles were identified plus 1 that is pending publication. Four articles were accounted for in this review, including 25 patients with newly diagnosed high-grade gliomas who underwent MR-LITT treatment. We evaluated safety, progression-free survival, and overall survival. RESULTS: Twenty-five patients with a mean age of 53.8 years underwent LITT treatments. On average, 82.9% of the pretreatment lesion volume was ablated. The average ...
Retroviruses specifically package full-length, dimeric genomic RNA (gRNA) even in the presence of... more Retroviruses specifically package full-length, dimeric genomic RNA (gRNA) even in the presence of a vast excess of cellular RNA. The "psi" (Ψ) element within the 5'-untranslated region (5'UTR) of gRNA is critical for packaging through interaction with the nucleocapsid (NC) domain of Gag. However, in vitro Gag binding affinity for Ψ versus non-Ψ RNAs is not significantly different. Previous salt-titration binding assays revealed that human immunodeficiency virus type 1 (HIV-1) Gag bound to Ψ RNA with high specificity and relatively few charge interactions, whereas binding to non-Ψ RNA was less specific and involved more electrostatic interactions. The NC domain was critical for specific Ψ binding, but surprisingly, a Gag mutant lacking the matrix (MA) domain was less effective at discriminating Ψ from non-Ψ RNA. We now find that Rous sarcoma virus (RSV) Gag also effectively discriminates RSV Ψ from non-Ψ RNA in a MA-dependent manner. Interestingly, Gag chimeras, whe...
Background: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result f... more Background: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in the gastrointestinal microbiome during IBD remain unclear. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics. Gene and pathway composition were assessed, based on 16S data from phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status. Results: Firmicutes and Enterobacteriaceae abundances were associated with disease status as expected, but also with treatment and subject characteristics. Microbial function, though, was more consistently perturbed than composition, with 12% of analyzed pathways changed compared with 2% of genera. We identified major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways. Conclusions: This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis.
A search for the standard model Higgs boson decaying into two Z bosons with subsequent decay into... more A search for the standard model Higgs boson decaying into two Z bosons with subsequent decay into a final state containing two quark jets and two leptons, H → ZZ(*) → q $ \overline {\text{q}} $ ℓ − ℓ + is presented. Results are based on data corresponding to an integrated luminosity of 4.6 fb−1 of proton-proton collisions at $ \sqrt {s} = 7 $ TeV, collected with the CMS detector at the LHC. In order to discriminate between signal and background events, kinematic and topological quantities, including the angular spin correlations of the decay products, are employed. Events are further classified according to the probability of the jets to originate from quarks of light or heavy flavor or from gluons. No evidence for the Higgs boson is found, and upper limits on its production cross section are determined for a Higgs boson of mass between 130 and 600 GeV.
Proceedings of the National Academy of Sciences, 2014
Significance Recent years have seen incredible growth in both the scale and specificity of projec... more Significance Recent years have seen incredible growth in both the scale and specificity of projects analyzing the microbial organisms living in and on the human body (the human microbiome). Such studies typically require subjects to report to clinics for sample collection, a complicated practice that is impractical for large studies. To address these issues, we developed a protocol that allows subjects to collect microbiome samples at home and ship them to laboratories for multiple different types of molecular analysis. Measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods. In addition, our subsequent analysis of these samples revealed interesting similarities and differences between the measured functional potential and functional activity of the human microbiome.
The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that... more The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.
ImportanceOphthalmology-residency selection committees require robust metrics to review applicant... more ImportanceOphthalmology-residency selection committees require robust metrics to review applicants. Participation in research activities is a core component of the application process for its perceived association with future academic productivity.ObjectiveTo evaluate the correlation between the number of preresidency peer-reviewed publications (PPPs) and subsequent peer-reviewed publications or career choices of ophthalmology residency graduates.Design, Setting, and ParticipantsIn this cross-sectional study, names of ophthalmology residency graduates were obtained. PubMed-indexed publication records were generated and publications were categorized as preresidency, intraresidency, and postresidency. First author and journal publications with an impact factor (IF) score of 3 or more were recorded. Current academic and community-based career statuses were designated. Names were obtained from cohort and alumni lists on residency program websites or by emailing program directors. Partic...
Purpose of Review In this article, we reviewed the impact resulting from the COVID-19 pandemic on... more Purpose of Review In this article, we reviewed the impact resulting from the COVID-19 pandemic on the traditional model of care in ophthalmology. Recent Findings Though virtual eye care has been present for more than 20 years, the COVID-19 pandemic has established a precedent to seriously consider its role in the evolving paradigm of vision and eye care. New hybrid models of care have enhanced or replaced traditional synchronous and asynchronous visits. The increased use of smart phoneography and mobile applications enhanced the remote examination of patients. Use of e-learning became a mainstream tool to continue accessing education and training. Summary Teleophthalmology has demonstrated its value for screening, examining, diagnosing, monitoring treatment, and increasing access to education. However, much of the progress made following the COVID-19 pandemic is at risk of being lost as society pushes to reestablish normalcy. Further studies during the new norm are required to prove a more permanent role for virtual eye care.
<p>(a) TD game: individuals make higher claims when the reward/punishment parameter is low,... more <p>(a) TD game: individuals make higher claims when the reward/punishment parameter is low, and make lower claims when is high. (b) MEC game: individuals expend more effort when the effort cost is low, and less effort when is high.</p
<p>(a)(c)(d)(e)(f) Average effort levels in the smoothed MEC game over the last of generati... more <p>(a)(c)(d)(e)(f) Average effort levels in the smoothed MEC game over the last of generations versus the effort cost parameter for different values of the smoothing parameter , on a complete graph (a), a random regular graph with degree 10 (c), a scale-free graph with mean degree 10 (d), 2D lattice graph with 4 neighbors (e), and 2D lattice graph with 8 neighbors (f). Parameter values: for lattice graphs and for other graphs, , and . (b) Number of individuals versus their effort levels , when and , on a complete graph with parameter values: , and .</p
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of micr... more Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function Users may view, print, copy, and download text and data-mine the content in such documents, for the...
effect of vibrotactile feedback on postural sway during locomotor activities (Article begins on n... more effect of vibrotactile feedback on postural sway during locomotor activities (Article begins on next page) The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters.
Purpose To describe the relationship between the number of Federal Drug Administration (FDA)-appr... more Purpose To describe the relationship between the number of Federal Drug Administration (FDA)-approved manufacturers and the price change of generic and branded topical eye drops. Methods Retrospective analysis of topical eye drop medications with formulations listed in the FDA Orange Book and the National Average Drug Acquisition Cost database from 2013 to 2017. Results The most frequently prescribed generic topical drugs were glaucoma medications (34%), antimicrobials (32%), anti-inflammatories (24%), mydriatics (5%), and anesthetics (5%). The most frequently prescribed branded topical drugs were anti-inflammatories (45%), glaucoma medications (32%), antimicrobials (21%) and dry eye medications (3%). From 2013 to 2017, generic eye drops had a median price decrease of 20% (IQR 32%) while branded eye drops had a median price increase of 44% (IQR 28%) (P < .001). A significant inverse association was identified between the price change of generic eye drops and the total number of a...
Cyanobacteria have multifaceted ecological roles on coral reefs. Moorena bouillonii, a chemically... more Cyanobacteria have multifaceted ecological roles on coral reefs. Moorena bouillonii, a chemically rich filamentous cyanobacterium, has been characterized as a pathogenic organism with an unusual ability to overgrow gorgonian corals, but little has been done to study its general growth habits or its unique association with the snapping shrimp Alpheus frontalis. Quantitative benthic surveys, and field and photographic observations were utilized to develop a better understanding of the ecology of these species, while growth experiments and nutrient analysis were performed to examine how this cyanobacterium may be benefiting from its shrimp symbiont. Colonies of M. bouillonii and A. frontalis displayed considerable habitat specificity in terms of occupied substrate. Although found to vary in abundance and density across survey sites and transects, M. bouillonii was consistently found to be thriving with A. frontalis within interstitial spaces on the reef. Removal of A. frontalis from cy...
OBJECTIVES: To determine the incidence of refeeding syndrome in otherwise healthy children <3 ... more OBJECTIVES: To determine the incidence of refeeding syndrome in otherwise healthy children <3 years of age admitted for failure to thrive (FTT). METHODS: A multicenter retrospective cohort study was performed on patients aged ≤36 months admitted with a primary diagnosis of FTT from January 1, 2011, to December 31, 2016. The primary outcome measure was the percentage of patients with laboratory evidence of refeeding syndrome. Exclusion criteria included admission to an ICU, parenteral nutrition, history of prematurity, gastrostomy tube feeds, and any complex chronic conditions. RESULTS: Of the 179 patients meeting inclusion criteria, none had laboratory evidence of refeeding syndrome. Of these, 145 (81%) had laboratory work done at the time of admission, and 69 (39%) had laboratory work repeated after admission. A small percentage (6%) of included patients experienced an adverse event due to repeat laboratory draw. CONCLUSIONS: In otherwise healthy hospitalized patients <3 year...
The tropical marine cyanobacterium Moorena bouillonii occupies a large geographic range across th... more The tropical marine cyanobacterium Moorena bouillonii occupies a large geographic range across the Indian and Western Tropical Pacific Oceans and is a prolific producer of structurally unique and biologically active natural products. An ensemble of computational approaches, including the creation of the ORCA (Objective Relational Comparative Analysis) pipeline for flexible MS1 feature detection and multivariate analyses, were used to analyze various M. bouillonii samples. The observed chemogeographic patterns suggested the production of regionally specific natural products by M. bouillonii. Analyzing the drivers of these chemogeographic patterns allowed for the identification, targeted isolation, and structure elucidation of a regionally specific natural product, doscadenamide A (1). Analyses of MS2 fragmentation patterns further revealed this natural product to be part of an extensive family of herein annotated, proposed natural structural analogs (doscadenamides B–J, 2–10); the en...
IOP Conference Series: Materials Science and Engineering, 2020
Philippines lie in the Pacific Ring of Fire, a region where earthquakes and other seismic activit... more Philippines lie in the Pacific Ring of Fire, a region where earthquakes and other seismic activities are frequent. Through the NBCDO Memorandum Circular No. 01 Series of 2015, The DPWH Guidelines and Implementing Rules on Earthquake Recording Instrumentation for buildings was implemented with the objectives of: (1) ensuring the safety of building occupants by determining the condition of buildings, and (2) collecting earthquake related data during major seismic activities. Despite being signed on March 12, 2015, the compliance rate of the buildings here in the City of Manila was low. The purpose of this study is to determine the cost impact of the said guidelines to building owners using MCDA-AHP; as well as to identify the amount needed to equip the City of Manila. The research was carried out having SHM experts (for AHP) and building owners (for MCDA) as the respondents for the corresponding parts of the study. The results show that the equipment price has the biggest impact to the building owners and their willingness to pay for ERIs is lower compared to the market.
BACKGROUND: Magnetic resonance-guided laser-interstitial thermotherapy (MR-LITT) is a minimally i... more BACKGROUND: Magnetic resonance-guided laser-interstitial thermotherapy (MR-LITT) is a minimally invasive technique that shows promise in neuro-oncology because of its superiority in delivering precise minimally invasive thermal energy with minimal collateral damage. OBJECTIVE: In this analysis, we investigate initial data on the use of MR-LITT in the treatment of newly diagnosed high-grade gliomas. METHODS: With the use of the PubMed, OVID, and Google-scholar database systems, a comprehensive search of the English literature was performed. Eighty-five articles were identified plus 1 that is pending publication. Four articles were accounted for in this review, including 25 patients with newly diagnosed high-grade gliomas who underwent MR-LITT treatment. We evaluated safety, progression-free survival, and overall survival. RESULTS: Twenty-five patients with a mean age of 53.8 years underwent LITT treatments. On average, 82.9% of the pretreatment lesion volume was ablated. The average ...
Retroviruses specifically package full-length, dimeric genomic RNA (gRNA) even in the presence of... more Retroviruses specifically package full-length, dimeric genomic RNA (gRNA) even in the presence of a vast excess of cellular RNA. The "psi" (Ψ) element within the 5'-untranslated region (5'UTR) of gRNA is critical for packaging through interaction with the nucleocapsid (NC) domain of Gag. However, in vitro Gag binding affinity for Ψ versus non-Ψ RNAs is not significantly different. Previous salt-titration binding assays revealed that human immunodeficiency virus type 1 (HIV-1) Gag bound to Ψ RNA with high specificity and relatively few charge interactions, whereas binding to non-Ψ RNA was less specific and involved more electrostatic interactions. The NC domain was critical for specific Ψ binding, but surprisingly, a Gag mutant lacking the matrix (MA) domain was less effective at discriminating Ψ from non-Ψ RNA. We now find that Rous sarcoma virus (RSV) Gag also effectively discriminates RSV Ψ from non-Ψ RNA in a MA-dependent manner. Interestingly, Gag chimeras, whe...
Background: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result f... more Background: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in the gastrointestinal microbiome during IBD remain unclear. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics. Gene and pathway composition were assessed, based on 16S data from phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status. Results: Firmicutes and Enterobacteriaceae abundances were associated with disease status as expected, but also with treatment and subject characteristics. Microbial function, though, was more consistently perturbed than composition, with 12% of analyzed pathways changed compared with 2% of genera. We identified major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways. Conclusions: This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis.
A search for the standard model Higgs boson decaying into two Z bosons with subsequent decay into... more A search for the standard model Higgs boson decaying into two Z bosons with subsequent decay into a final state containing two quark jets and two leptons, H → ZZ(*) → q $ \overline {\text{q}} $ ℓ − ℓ + is presented. Results are based on data corresponding to an integrated luminosity of 4.6 fb−1 of proton-proton collisions at $ \sqrt {s} = 7 $ TeV, collected with the CMS detector at the LHC. In order to discriminate between signal and background events, kinematic and topological quantities, including the angular spin correlations of the decay products, are employed. Events are further classified according to the probability of the jets to originate from quarks of light or heavy flavor or from gluons. No evidence for the Higgs boson is found, and upper limits on its production cross section are determined for a Higgs boson of mass between 130 and 600 GeV.
Proceedings of the National Academy of Sciences, 2014
Significance Recent years have seen incredible growth in both the scale and specificity of projec... more Significance Recent years have seen incredible growth in both the scale and specificity of projects analyzing the microbial organisms living in and on the human body (the human microbiome). Such studies typically require subjects to report to clinics for sample collection, a complicated practice that is impractical for large studies. To address these issues, we developed a protocol that allows subjects to collect microbiome samples at home and ship them to laboratories for multiple different types of molecular analysis. Measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods. In addition, our subsequent analysis of these samples revealed interesting similarities and differences between the measured functional potential and functional activity of the human microbiome.
The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that... more The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.
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Papers by Joshua Reyes