2020 11th IEEE Annual Information Technology, Electronics and Mobile Communication Conference (IEMCON), 2020
The 4-gram would be "I went to work" 4) Prune the list of candidate aspects in order to create a ... more The 4-gram would be "I went to work" 4) Prune the list of candidate aspects in order to create a more-relevant list of aspects 5) Cross compare the pruned aspects to the original data in order to find sentimental connections between the data.
Tocotrienols, components of vitamin E, may have beneficial effects on vascular function in pathol... more Tocotrienols, components of vitamin E, may have beneficial effects on vascular function in pathologies involving oxidant stress eg: diabetes. Tocomin (Toc) is an extract of palm oil with high tocotrienol content. We investigated the effect of acute Toc (10-4 mg/mL) treatment on endothelium-dependent relaxation (EDR) and superoxide (O2-) production in aortae from diabetic rats and rats fed a standard (SD) or western (WD) diet. Wistar rats were treated with vehicle (control (C)) or streptozotocin (50 mg/kg iv) to induce diabetes (D) for 10 weeks. Wistar Hooded rats were fed SD (7% total fat) or WD (21% total fat). Rats were fed ad lib for 7 weeks after which they were placed on a restricted diet (70% of normal consumption for 10 weeks). EDR and O2- were measured using standard organ bath techniques and enhanced chemiluminescence. Diabetes impaired EDR which improved with Toc treatment (ACh Rmax C 855% vs D 644% vs D+T 873%, p0.05), whereas WD reduced ACh sensitivity that improved with Toc treatment (ACh pEC...
AbstractThis research applies basic parameters of sustainable architecture to study the social ho... more AbstractThis research applies basic parameters of sustainable architecture to study the social housing neighborhoods in the city of Palmira (Colombia) in order to identify their main problems relat...
Phase transition temperatures (°C) and enthalpies (in parentheses, kJ/mol). Heating and cooling r... more Phase transition temperatures (°C) and enthalpies (in parentheses, kJ/mol). Heating and cooling rates of 10 °C/min. Monotropic transitions are given in brackets. OC4 Ph(mono(3,5diMe)ODBP) Cr 172 (50.8) N 206.2 (1.47) I OC4 2MePh(mono(3,5diMe)ODBP) Cr 136 (39.0) I [I 96.7 (0.83) N] OC4 3MePh(mono(3,5diMe)ODBP) Cr 135 a Cr2 153.4 (47.4) I [I 125.2 (1.38) N] OC4 Ph(3MeODBP) Cr 147.9 (51.3) N 209.5 (1.44) I OC4 2MePh(3MeODBP) Cr 149.3 (54.9) I [I 94.4 (0.91) N] OC4 3MePh(3MeODBP) Cr 144.4 (1.60) Cr2 161.8 (56.3) I [I 133.5 (2.1) N 73.5 (5.71) Cr] a Because the endothermic peak at 135 °C is followed immediately by an exothermic peak, no enthalpy for this transition could be determined.
This paper analyzes the energy efficiency (EE) investment decisions of a capital-constrained manu... more This paper analyzes the energy efficiency (EE) investment decisions of a capital-constrained manufacturer that competes with an alternative supplier for the business of a large industrial buyer. Through a series of game-theoretic models, we characterize when it is beneficial for the buyer to offer EE instruments, including assessment assistance and procurement commitment, and how these instruments interact with third-party assessment assistance to affect the supplier’s EE investment level. We find that assessment assistance helps reduce the EE gap but procurement commitment is required to eliminate it. We also find that the availability of third-party assessment assistance reduces the buyer’s incentive to offer both of its instruments, a scenario that potentially lowers the supplier’s EE investment level. Our findings provide insights for buyers and policy makers interested in improving supply-chain EE. The online appendix is available at https://doi.org/10.1287/mnsc.2017.2941 . Thi...
Purpose: Sphingolipids (SPL) play roles in cell signaling, inflammation, and apoptosis. Changes i... more Purpose: Sphingolipids (SPL) play roles in cell signaling, inflammation, and apoptosis. Changes in SPL composition have been reported in individuals with MGD, but associations between clinical signs of MGD and compositional changes in meibum SPLs have not been examined. Methods: Forty-three individuals underwent a tear film assessment. Groups were split into those with good or poor quality meibum. Meibum was collected then analyzed with liquid chromatography-mass spectroscopy to quantify SPL classes. Relative composition of SPL and major classes, Ceramide (Cer), Hexosyl-Ceramide (Hex-Cer), Sphingomyelin (SM), Sphingosine (Sph) and Sphingosine 1-phosphate (S1P) was calculated via mole percent. Results: 22 and 21 individuals were characterized with good and poor quality meibum, respectively. Individuals with poor quality were older (60 ± 8 vs 51 ± 16 years) and more likely to be male (90% vs 64%). Relative composition analysis revealed that individuals with poor meibum *
Journal of cataract and refractive surgery, Jan 20, 2018
To evaluate long-term capsular clarity with a modified disk-shaped 1-piece hydrophilic acrylic mo... more To evaluate long-term capsular clarity with a modified disk-shaped 1-piece hydrophilic acrylic monofocal intraocular lens (IOL) (Zephyr) suspended between 2 complete haptic rings connected by a pillar of the haptic material. John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, USA. Experimental study. Study and control (1-piece hydrophobic acrylic) IOLs were implanted into the right and left eyes, respectively, of 8 New Zealand rabbits. Eyes were examined at the slitlamp at set intervals for 6 months. At the end of the clinical follow-up, the globes were enucleated and capsular clarity was scored from the posterior view (Miyake-Apple technique). Then, all the eyes were processed for a complete histopathological evaluation. At 6 months, the slitlamp evaluation showed a posterior capsule opacification score of 0.28 ± 0.26 (SD) in the study group and 4 ± 0 in the control (P < .0001, paired t test). The anterior capsule was generally clear in the study group. This para...
Pulmonary arterial hypertension (PAH) is a chronic pulmonary vascular disease characterized by in... more Pulmonary arterial hypertension (PAH) is a chronic pulmonary vascular disease characterized by increased pulmonary vascular resistance (PVR) leading to right ventricular (RV) failure. Autonomic nervous system involvement in the pathogenesis of PAH has been demonstrated several years ago, however the extent of this involvement is not fully understood. PAH is associated with increased sympathetic nervous system (SNS) activation, decreased heart rate variability, and presence of cardiac arrhythmias. There is also evidence for increased renin-angiotensin-aldosterone system (RAAS) activation in PAH patients associated with clinical worsening. Reduction of neurohormonal activation could be an effective therapeutic strategy for PAH. Although therapies targeting adrenergic receptors or RAAS signaling pathways have been shown to reverse cardiac remodeling and improve outcomes in experimental pulmonary hypertension (PH)-models, the effectiveness and safety of such treatments in clinical setti...
To evaluate the biocompatibility (uveal and capsular) of intraocular lens (IOL) power adjustment ... more To evaluate the biocompatibility (uveal and capsular) of intraocular lens (IOL) power adjustment by a femtosecond laser obtained through increased hydrophilicity of targeted areas within the optic, creating the ability to build a refractive-index shaping lens within an existing IOL.
Learning and Collaboration Technologies. Ubiquitous and Virtual Environments for Learning and Collaboration, 2019
While increases in the development of virtual reality (VR) have expanded the possibilities of lea... more While increases in the development of virtual reality (VR) have expanded the possibilities of learning foreign languages, research for computer assisted language learning in VR is lacking [1]. Virtual reality headsets continue to become more accessible to end users, and there is a current lack of educational language learning applications for such platforms. There are many tools and applications for language learning, however most lack the aspect of immersion – a proven method of learning a foreign language as seen in experiments involving overseas language experiences [2]. Therefore, this paper presents an interactive VR experience for learning Spanish through an immersive interaction and game-play, followed by the results from a focus group regarding user experience feedback. Additionally, this paper will detail the design and development of the current prototype. Results indicate that participants found this method of language learning to be more enjoyable than traditional methods because it did not feel like they were studying.
International Journal of Infectious Diseases, 2021
Mutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to gener... more Mutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to generate high-quality genome sequences for COVID-19 surveillance. Here, we identify 46 mutations in current variant of concern lineages affecting the widely used laboratory protocols for SARS-CoV-2 genomic sequencing by Freed et al. and the ARTIC network. We provide laboratory data showing how three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada, and we also demonstrate how we modified the Freed et al. protocol to restore performance. Background Genomic sequencing of SARS coronavirus-2 (SARS-CoV-2) has played a crucial role in managing the ongoing COVID-19 pandemic. This is especially true for variant of concern lineages that have emerged globally since December 2020 [1-6]. Genomic sequencing has been instrumental in detecting and characterizing these lineages as they emerge, tracking their global spread, and identifying local cases to control transmission. Due to low quantities of viral genomic material in typical clinical specimens, the SARS-CoV-2 genome must be amplified for high-throughput sequencing. This is commonly done by amplicon sequencing. This approach involves multiplexed PCR with numerous primers pairs tiled across the viral genome [7-9]. The performance of these primer schemes can be impacted by mutations associated with emerging viral lineages. These mutations create thermodynamic instabilities between primer oligonucleotides and genomic template material, interfering with amplification. This causes drop-outs in sequencing coverage and hinders the collection of complete, high-quality viral genomes. Amplicon drop-outs in P.1 lineage specimens using the Freed et al. primer scheme The British Columbia Centre for Disease Control's Public Health Laboratory (BCCDC PHL) currently uses the 1200 bp amplicon scheme by Freed et al. for genomic sequencing of SARS-CoV-2 clinical specimens [8]. While investigating a local P.1 lineage outbreak in March and April 2021, the BCCDC PHL observed significantly reduced depth of coverage across three amplicons covering parts of the orf1ab and spike genes (Figure 1). This suggested that mutations in the P.1 lineage had occurred in primer sites targeted by the Freed et al. amplicon scheme.
The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagn... more The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity. .
Background Measuring routine childhood vaccination is crucial to inform global vaccine policies a... more Background Measuring routine childhood vaccination is crucial to inform global vaccine policies and programme implementation, and to track progress towards targets set by the Global Vaccine Action Plan (GVAP) and Immunization Agenda 2030. Robust estimates of routine vaccine coverage are needed to identify past successes and persistent vulnerabilities. Drawing from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2020, Release 1, we did a systematic analysis of global, regional, and national vaccine coverage trends using a statistical framework, by vaccine and over time. Methods For this analysis we collated 55 326 country-specific, cohort-specific, year-specific, vaccine-specific, and dose-specific observations of routine childhood vaccination coverage between 1980 and 2019. Using spatiotemporal Gaussian process regression, we produced location-specific and year-specific estimates of 11 routine childhood vaccine coverage indicators for 204 countries and territories from 1980 to 2019, adjusting for biases in country-reported data and reflecting reported stockouts and supply disruptions. We analysed global and regional trends in coverage and numbers of zero-dose children (defined as those who never received a diphtheria-tetanus-pertussis [DTP] vaccine dose), progress towards GVAP targets, and the relationship between vaccine coverage and sociodemographic development. Findings By 2019, global coverage of third-dose DTP (DTP3; 81·6% [95% uncertainty interval 80·4–82·7]) more than doubled from levels estimated in 1980 (39·9% [37·5–42·1]), as did global coverage of the first-dose measles-containing vaccine (MCV1; from 38·5% [35·4–41·3] in 1980 to 83·6% [82·3–84·8] in 2019). Third-dose polio vaccine (Pol3) coverage also increased, from 42·6% (41·4–44·1) in 1980 to 79·8% (78·4–81·1) in 2019, and global coverage of newer vaccines increased rapidly between 2000 and 2019. The global number of zero-dose children fell by nearly 75% between 1980 and 2019, from 56·8 million (52·6–60·9) to 14·5 million (13·4–15·9). However, over the past decade, global vaccine coverage broadly plateaued; 94 countries and territories recorded decreasing DTP3 coverage since 2010. Only 11 countries and territories were estimated to have reached the national GVAP target of at least 90% coverage for all assessed vaccines in 2019. Interpretation After achieving large gains in childhood vaccine coverage worldwide, in much of the world this progress was stalled or reversed from 2010 to 2019. These findings underscore the importance of revisiting routine immunisation strategies and programmatic approaches, recentring service delivery around equity and underserved populations. Strengthening vaccine data and monitoring systems is crucial to these pursuits, now and through to 2030, to ensure that all children have access to, and can benefit from, lifesaving vaccines. Funding Bill & Melinda Gates Foundation
We present charged-particle distributions sensitive to the underlying event, measured by the ATLA... more We present charged-particle distributions sensitive to the underlying event, measured by the ATLAS detector in proton-proton collisions at a centre-of-mass energy of 13 TeV, in low-luminosity Large Hadron Collider fills corresponding to an integrated luminosity of 1.6 nb −1. The distributions were constructed using charged particles with absolute pseudorapidity less than 2.5 and with transverse momentum greater than 500 MeV, in events with at least one such charged particle with transverse momentum above 1 GeV. These distributions characterise the angular distribution of energy and particle flows with respect to the charged particle with highest transverse momentum, as a function of both that momentum and of charged-particle multiplicity. The results have been corrected for detector effects and are compared to the predictions of various Monte Carlo event generators, experimentally establishing the level of underlying-event activity at LHC Run 2 energies and providing inputs for the development of event generator modelling. The current models in use for UE modelling typically describe this data to 5% accuracy, compared with data uncertainties of less than 1%.
Extended Abstracts of the 2019 CHI Conference on Human Factors in Computing Systems, 2019
This demo showcases an interactive virtual reality experience for language learning that allows u... more This demo showcases an interactive virtual reality experience for language learning that allows users to enter a virtual world to explore and interact with their surroundings while learning Spanish. Through immersive game-play on the Oculus Rift, users explore Spanish translations of everyday household items in a search-and-find format, scoring points when they can correctly identify and select objects. Users are able to put what they learn into practice in real time. Study participants who tried the experience said they found this method of language learning to be more enjoyable than traditional methods of studying due to the gamification created and it not "feeling like studying". As virtual reality headsets continue to become more accessible to the public, addresses the cost limitations of traveling overseas to achieve immersion in foreign language. This application can be expanded to most real-world scenarios and locations. Additionally, it can be applied to any language.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
The efficiency to identify jets containing b-hadrons (b-jets) is measured using a high purity sam... more The efficiency to identify jets containing b-hadrons (b-jets) is measured using a high purity sample of dileptonic top quark-antiquark pairs ( $$ t\\overline{t} $$ t t ¯ ) selected from the 36.1 fb−1 of data collected by the ATLAS detector in 2015 and 2016 from proton-proton collisions produced by the Large Hadron Collider at a centre-of-mass energy $$ \\sqrt{s}=13 $$ s = 13 TeV. Two methods are used to extract the efficiency from $$ t\\overline{t} $$ t t ¯ events, a combinatorial likelihood approach and a tag-and-probe method. A boosted decision tree, not using b-tagging information, is used to select events in which two b-jets are present, which reduces the dominant uncertainty in the modelling of the flavour of the jets. The efficiency is extracted for jets in a transverse momentum range from 20 to 300 GeV, with data-to-simulation scale factors calculated by comparing the efficiency measured using collision data to that predicted by the simulation. The two methods give compatible re...
2020 11th IEEE Annual Information Technology, Electronics and Mobile Communication Conference (IEMCON), 2020
The 4-gram would be "I went to work" 4) Prune the list of candidate aspects in order to create a ... more The 4-gram would be "I went to work" 4) Prune the list of candidate aspects in order to create a more-relevant list of aspects 5) Cross compare the pruned aspects to the original data in order to find sentimental connections between the data.
Tocotrienols, components of vitamin E, may have beneficial effects on vascular function in pathol... more Tocotrienols, components of vitamin E, may have beneficial effects on vascular function in pathologies involving oxidant stress eg: diabetes. Tocomin (Toc) is an extract of palm oil with high tocotrienol content. We investigated the effect of acute Toc (10-4 mg/mL) treatment on endothelium-dependent relaxation (EDR) and superoxide (O2-) production in aortae from diabetic rats and rats fed a standard (SD) or western (WD) diet. Wistar rats were treated with vehicle (control (C)) or streptozotocin (50 mg/kg iv) to induce diabetes (D) for 10 weeks. Wistar Hooded rats were fed SD (7% total fat) or WD (21% total fat). Rats were fed ad lib for 7 weeks after which they were placed on a restricted diet (70% of normal consumption for 10 weeks). EDR and O2- were measured using standard organ bath techniques and enhanced chemiluminescence. Diabetes impaired EDR which improved with Toc treatment (ACh Rmax C 855% vs D 644% vs D+T 873%, p0.05), whereas WD reduced ACh sensitivity that improved with Toc treatment (ACh pEC...
AbstractThis research applies basic parameters of sustainable architecture to study the social ho... more AbstractThis research applies basic parameters of sustainable architecture to study the social housing neighborhoods in the city of Palmira (Colombia) in order to identify their main problems relat...
Phase transition temperatures (°C) and enthalpies (in parentheses, kJ/mol). Heating and cooling r... more Phase transition temperatures (°C) and enthalpies (in parentheses, kJ/mol). Heating and cooling rates of 10 °C/min. Monotropic transitions are given in brackets. OC4 Ph(mono(3,5diMe)ODBP) Cr 172 (50.8) N 206.2 (1.47) I OC4 2MePh(mono(3,5diMe)ODBP) Cr 136 (39.0) I [I 96.7 (0.83) N] OC4 3MePh(mono(3,5diMe)ODBP) Cr 135 a Cr2 153.4 (47.4) I [I 125.2 (1.38) N] OC4 Ph(3MeODBP) Cr 147.9 (51.3) N 209.5 (1.44) I OC4 2MePh(3MeODBP) Cr 149.3 (54.9) I [I 94.4 (0.91) N] OC4 3MePh(3MeODBP) Cr 144.4 (1.60) Cr2 161.8 (56.3) I [I 133.5 (2.1) N 73.5 (5.71) Cr] a Because the endothermic peak at 135 °C is followed immediately by an exothermic peak, no enthalpy for this transition could be determined.
This paper analyzes the energy efficiency (EE) investment decisions of a capital-constrained manu... more This paper analyzes the energy efficiency (EE) investment decisions of a capital-constrained manufacturer that competes with an alternative supplier for the business of a large industrial buyer. Through a series of game-theoretic models, we characterize when it is beneficial for the buyer to offer EE instruments, including assessment assistance and procurement commitment, and how these instruments interact with third-party assessment assistance to affect the supplier’s EE investment level. We find that assessment assistance helps reduce the EE gap but procurement commitment is required to eliminate it. We also find that the availability of third-party assessment assistance reduces the buyer’s incentive to offer both of its instruments, a scenario that potentially lowers the supplier’s EE investment level. Our findings provide insights for buyers and policy makers interested in improving supply-chain EE. The online appendix is available at https://doi.org/10.1287/mnsc.2017.2941 . Thi...
Purpose: Sphingolipids (SPL) play roles in cell signaling, inflammation, and apoptosis. Changes i... more Purpose: Sphingolipids (SPL) play roles in cell signaling, inflammation, and apoptosis. Changes in SPL composition have been reported in individuals with MGD, but associations between clinical signs of MGD and compositional changes in meibum SPLs have not been examined. Methods: Forty-three individuals underwent a tear film assessment. Groups were split into those with good or poor quality meibum. Meibum was collected then analyzed with liquid chromatography-mass spectroscopy to quantify SPL classes. Relative composition of SPL and major classes, Ceramide (Cer), Hexosyl-Ceramide (Hex-Cer), Sphingomyelin (SM), Sphingosine (Sph) and Sphingosine 1-phosphate (S1P) was calculated via mole percent. Results: 22 and 21 individuals were characterized with good and poor quality meibum, respectively. Individuals with poor quality were older (60 ± 8 vs 51 ± 16 years) and more likely to be male (90% vs 64%). Relative composition analysis revealed that individuals with poor meibum *
Journal of cataract and refractive surgery, Jan 20, 2018
To evaluate long-term capsular clarity with a modified disk-shaped 1-piece hydrophilic acrylic mo... more To evaluate long-term capsular clarity with a modified disk-shaped 1-piece hydrophilic acrylic monofocal intraocular lens (IOL) (Zephyr) suspended between 2 complete haptic rings connected by a pillar of the haptic material. John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, USA. Experimental study. Study and control (1-piece hydrophobic acrylic) IOLs were implanted into the right and left eyes, respectively, of 8 New Zealand rabbits. Eyes were examined at the slitlamp at set intervals for 6 months. At the end of the clinical follow-up, the globes were enucleated and capsular clarity was scored from the posterior view (Miyake-Apple technique). Then, all the eyes were processed for a complete histopathological evaluation. At 6 months, the slitlamp evaluation showed a posterior capsule opacification score of 0.28 ± 0.26 (SD) in the study group and 4 ± 0 in the control (P < .0001, paired t test). The anterior capsule was generally clear in the study group. This para...
Pulmonary arterial hypertension (PAH) is a chronic pulmonary vascular disease characterized by in... more Pulmonary arterial hypertension (PAH) is a chronic pulmonary vascular disease characterized by increased pulmonary vascular resistance (PVR) leading to right ventricular (RV) failure. Autonomic nervous system involvement in the pathogenesis of PAH has been demonstrated several years ago, however the extent of this involvement is not fully understood. PAH is associated with increased sympathetic nervous system (SNS) activation, decreased heart rate variability, and presence of cardiac arrhythmias. There is also evidence for increased renin-angiotensin-aldosterone system (RAAS) activation in PAH patients associated with clinical worsening. Reduction of neurohormonal activation could be an effective therapeutic strategy for PAH. Although therapies targeting adrenergic receptors or RAAS signaling pathways have been shown to reverse cardiac remodeling and improve outcomes in experimental pulmonary hypertension (PH)-models, the effectiveness and safety of such treatments in clinical setti...
To evaluate the biocompatibility (uveal and capsular) of intraocular lens (IOL) power adjustment ... more To evaluate the biocompatibility (uveal and capsular) of intraocular lens (IOL) power adjustment by a femtosecond laser obtained through increased hydrophilicity of targeted areas within the optic, creating the ability to build a refractive-index shaping lens within an existing IOL.
Learning and Collaboration Technologies. Ubiquitous and Virtual Environments for Learning and Collaboration, 2019
While increases in the development of virtual reality (VR) have expanded the possibilities of lea... more While increases in the development of virtual reality (VR) have expanded the possibilities of learning foreign languages, research for computer assisted language learning in VR is lacking [1]. Virtual reality headsets continue to become more accessible to end users, and there is a current lack of educational language learning applications for such platforms. There are many tools and applications for language learning, however most lack the aspect of immersion – a proven method of learning a foreign language as seen in experiments involving overseas language experiences [2]. Therefore, this paper presents an interactive VR experience for learning Spanish through an immersive interaction and game-play, followed by the results from a focus group regarding user experience feedback. Additionally, this paper will detail the design and development of the current prototype. Results indicate that participants found this method of language learning to be more enjoyable than traditional methods because it did not feel like they were studying.
International Journal of Infectious Diseases, 2021
Mutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to gener... more Mutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to generate high-quality genome sequences for COVID-19 surveillance. Here, we identify 46 mutations in current variant of concern lineages affecting the widely used laboratory protocols for SARS-CoV-2 genomic sequencing by Freed et al. and the ARTIC network. We provide laboratory data showing how three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada, and we also demonstrate how we modified the Freed et al. protocol to restore performance. Background Genomic sequencing of SARS coronavirus-2 (SARS-CoV-2) has played a crucial role in managing the ongoing COVID-19 pandemic. This is especially true for variant of concern lineages that have emerged globally since December 2020 [1-6]. Genomic sequencing has been instrumental in detecting and characterizing these lineages as they emerge, tracking their global spread, and identifying local cases to control transmission. Due to low quantities of viral genomic material in typical clinical specimens, the SARS-CoV-2 genome must be amplified for high-throughput sequencing. This is commonly done by amplicon sequencing. This approach involves multiplexed PCR with numerous primers pairs tiled across the viral genome [7-9]. The performance of these primer schemes can be impacted by mutations associated with emerging viral lineages. These mutations create thermodynamic instabilities between primer oligonucleotides and genomic template material, interfering with amplification. This causes drop-outs in sequencing coverage and hinders the collection of complete, high-quality viral genomes. Amplicon drop-outs in P.1 lineage specimens using the Freed et al. primer scheme The British Columbia Centre for Disease Control's Public Health Laboratory (BCCDC PHL) currently uses the 1200 bp amplicon scheme by Freed et al. for genomic sequencing of SARS-CoV-2 clinical specimens [8]. While investigating a local P.1 lineage outbreak in March and April 2021, the BCCDC PHL observed significantly reduced depth of coverage across three amplicons covering parts of the orf1ab and spike genes (Figure 1). This suggested that mutations in the P.1 lineage had occurred in primer sites targeted by the Freed et al. amplicon scheme.
The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagn... more The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity. .
Background Measuring routine childhood vaccination is crucial to inform global vaccine policies a... more Background Measuring routine childhood vaccination is crucial to inform global vaccine policies and programme implementation, and to track progress towards targets set by the Global Vaccine Action Plan (GVAP) and Immunization Agenda 2030. Robust estimates of routine vaccine coverage are needed to identify past successes and persistent vulnerabilities. Drawing from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2020, Release 1, we did a systematic analysis of global, regional, and national vaccine coverage trends using a statistical framework, by vaccine and over time. Methods For this analysis we collated 55 326 country-specific, cohort-specific, year-specific, vaccine-specific, and dose-specific observations of routine childhood vaccination coverage between 1980 and 2019. Using spatiotemporal Gaussian process regression, we produced location-specific and year-specific estimates of 11 routine childhood vaccine coverage indicators for 204 countries and territories from 1980 to 2019, adjusting for biases in country-reported data and reflecting reported stockouts and supply disruptions. We analysed global and regional trends in coverage and numbers of zero-dose children (defined as those who never received a diphtheria-tetanus-pertussis [DTP] vaccine dose), progress towards GVAP targets, and the relationship between vaccine coverage and sociodemographic development. Findings By 2019, global coverage of third-dose DTP (DTP3; 81·6% [95% uncertainty interval 80·4–82·7]) more than doubled from levels estimated in 1980 (39·9% [37·5–42·1]), as did global coverage of the first-dose measles-containing vaccine (MCV1; from 38·5% [35·4–41·3] in 1980 to 83·6% [82·3–84·8] in 2019). Third-dose polio vaccine (Pol3) coverage also increased, from 42·6% (41·4–44·1) in 1980 to 79·8% (78·4–81·1) in 2019, and global coverage of newer vaccines increased rapidly between 2000 and 2019. The global number of zero-dose children fell by nearly 75% between 1980 and 2019, from 56·8 million (52·6–60·9) to 14·5 million (13·4–15·9). However, over the past decade, global vaccine coverage broadly plateaued; 94 countries and territories recorded decreasing DTP3 coverage since 2010. Only 11 countries and territories were estimated to have reached the national GVAP target of at least 90% coverage for all assessed vaccines in 2019. Interpretation After achieving large gains in childhood vaccine coverage worldwide, in much of the world this progress was stalled or reversed from 2010 to 2019. These findings underscore the importance of revisiting routine immunisation strategies and programmatic approaches, recentring service delivery around equity and underserved populations. Strengthening vaccine data and monitoring systems is crucial to these pursuits, now and through to 2030, to ensure that all children have access to, and can benefit from, lifesaving vaccines. Funding Bill & Melinda Gates Foundation
We present charged-particle distributions sensitive to the underlying event, measured by the ATLA... more We present charged-particle distributions sensitive to the underlying event, measured by the ATLAS detector in proton-proton collisions at a centre-of-mass energy of 13 TeV, in low-luminosity Large Hadron Collider fills corresponding to an integrated luminosity of 1.6 nb −1. The distributions were constructed using charged particles with absolute pseudorapidity less than 2.5 and with transverse momentum greater than 500 MeV, in events with at least one such charged particle with transverse momentum above 1 GeV. These distributions characterise the angular distribution of energy and particle flows with respect to the charged particle with highest transverse momentum, as a function of both that momentum and of charged-particle multiplicity. The results have been corrected for detector effects and are compared to the predictions of various Monte Carlo event generators, experimentally establishing the level of underlying-event activity at LHC Run 2 energies and providing inputs for the development of event generator modelling. The current models in use for UE modelling typically describe this data to 5% accuracy, compared with data uncertainties of less than 1%.
Extended Abstracts of the 2019 CHI Conference on Human Factors in Computing Systems, 2019
This demo showcases an interactive virtual reality experience for language learning that allows u... more This demo showcases an interactive virtual reality experience for language learning that allows users to enter a virtual world to explore and interact with their surroundings while learning Spanish. Through immersive game-play on the Oculus Rift, users explore Spanish translations of everyday household items in a search-and-find format, scoring points when they can correctly identify and select objects. Users are able to put what they learn into practice in real time. Study participants who tried the experience said they found this method of language learning to be more enjoyable than traditional methods of studying due to the gamification created and it not "feeling like studying". As virtual reality headsets continue to become more accessible to the public, addresses the cost limitations of traveling overseas to achieve immersion in foreign language. This application can be expanded to most real-world scenarios and locations. Additionally, it can be applied to any language.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
The efficiency to identify jets containing b-hadrons (b-jets) is measured using a high purity sam... more The efficiency to identify jets containing b-hadrons (b-jets) is measured using a high purity sample of dileptonic top quark-antiquark pairs ( $$ t\\overline{t} $$ t t ¯ ) selected from the 36.1 fb−1 of data collected by the ATLAS detector in 2015 and 2016 from proton-proton collisions produced by the Large Hadron Collider at a centre-of-mass energy $$ \\sqrt{s}=13 $$ s = 13 TeV. Two methods are used to extract the efficiency from $$ t\\overline{t} $$ t t ¯ events, a combinatorial likelihood approach and a tag-and-probe method. A boosted decision tree, not using b-tagging information, is used to select events in which two b-jets are present, which reduces the dominant uncertainty in the modelling of the flavour of the jets. The efficiency is extracted for jets in a transverse momentum range from 20 to 300 GeV, with data-to-simulation scale factors calculated by comparing the efficiency measured using collision data to that predicted by the simulation. The two methods give compatible re...
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