This document reports on the detection of Berry's phase in the bulk Rashba semiconductor bismuth telluride iodide (BiTeI). The researchers analyzed Shubnikov-de Haas oscillations from spin-split inner and outer Fermi surfaces in BiTeI under an external magnetic field. They observed a systematic pi-phase shift in the oscillations from both Fermi surfaces, consistent with the theoretically predicted non-trivial pi Berry's phase in Rashba systems. This provides direct experimental evidence of a non-trivial Berry's phase in the bulk states of a physical-spin Rashba system.
Baryons at the edge of the x ray–brightest galaxy clusterSérgio Sacani
This article discusses observations of the outskirts of the Perseus galaxy cluster, which is the brightest extended X-ray source. The observations find evidence of gas beyond the virial radius that has been shock heated to high temperatures by accretion and mergers. The results provide insights into the formation and evolution of large-scale structure in the universe.
Comparing the Amount and Quality of Information from Different Sequencing Str...jembrown
This document compares the amount and quality of phylogenetic information from six amniote phylogenomic datasets. It finds that while median support for major relationships is often strong, there is wide variance in support, both for and against known relationships. This suggests a minimum level of systematic error. Support for turtle placement varies the most between datasets, indicating relatively little phylogenetic information about turtles compared to other amniote groups. Overall, the analysis demonstrates that phylogenomic datasets can differ substantially in information content and reliability.
The document summarizes a talk on microbial agrogenomics. It discusses how genomics has advanced the understanding of plant-microbe interactions in several ways:
1) Genomes allow cataloging of genes and features in organisms and comparing common features between organisms that associate with phenotypes.
2) Multiple pathogen and plant genomes have enabled studying epidemiology through tracing historical origins, emergence in new areas, and host jumps.
3) Genomics provides diagnostic tools for precise pathogen identification needed for quarantine and legislation.
Mingdong_research focus with references 2017.01Mingdong Huang
The document summarizes the author's recent research focusing on three directions: (1) studying the structures and functions of fibrinolytic proteins and developing inhibitors for them, (2) determining the structures of cell surface receptors and human serum albumin, and (3) developing a fluorescent probe for biomedical imaging, cancer therapy, and antimicrobial applications by conjugating it to targeting peptides. The author has determined several protein crystal structures and developed peptide inhibitors for proteases involved in cancer metastasis. The fluorescent probe conjugates show tumor targeting capability in mouse models and effectiveness against drug resistant bacteria.
This document provides a bibliography or list of references for the topic of "Identification and Validation of Drug Targets". It includes over 150 references in APA citation format from various sources like published papers, patents, books and reports. The references are grouped alphabetically and provide information to support further research on drug target identification and validation methods.
This article reports the detection of two gas clouds with no discernible elements heavier than hydrogen, representing the lowest heavy-element abundance observed in the early universe. One cloud at z=3.4 exhibits a deuterium abundance matching predictions from Big Bang nucleosynthesis, providing direct evidence for the standard cosmological model. The sparse metal enrichment of these clouds implies an inhomogeneous process for transporting heavy elements from galaxies into the surrounding intergalactic medium.
This curriculum vitae summarizes the academic and employment history, education, research activities, and publications of Joshua Harris Singer. Some key details include:
- Singer is currently an Associate Professor in the Department of Biology at the University of Maryland. He was previously an Assistant Professor at Northwestern University and UMD.
- He received a ScB in Biology from Brown University and a PhD in Physiology from the University of Washington.
- His research focuses on synaptic transmission and retinal circuit function, as evidenced by over 25 peer-reviewed publications on these topics. He has also given numerous invited talks on his research.
CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis...Surya Saha
CitrusCyc is a metabolic pathway database for the Citrus clementina and Citrus sinensis genomes. It was constructed using the Pathway Tools software and contains pathways, reactions, enzymes and genes derived from the annotated citrus genomes and the MetaCyc database. The database contains over 25,000 proteins and 40,000 transcripts with EC numbers for both citrus species. It provides visualizations of metabolic pathways and allows for overlay of RNA-seq expression data. Future work includes manual curation of pathways and development of a Meta-CitrusCyc database.
Baryons at the edge of the x ray–brightest galaxy clusterSérgio Sacani
This article discusses observations of the outskirts of the Perseus galaxy cluster, which is the brightest extended X-ray source. The observations find evidence of gas beyond the virial radius that has been shock heated to high temperatures by accretion and mergers. The results provide insights into the formation and evolution of large-scale structure in the universe.
Comparing the Amount and Quality of Information from Different Sequencing Str...jembrown
This document compares the amount and quality of phylogenetic information from six amniote phylogenomic datasets. It finds that while median support for major relationships is often strong, there is wide variance in support, both for and against known relationships. This suggests a minimum level of systematic error. Support for turtle placement varies the most between datasets, indicating relatively little phylogenetic information about turtles compared to other amniote groups. Overall, the analysis demonstrates that phylogenomic datasets can differ substantially in information content and reliability.
The document summarizes a talk on microbial agrogenomics. It discusses how genomics has advanced the understanding of plant-microbe interactions in several ways:
1) Genomes allow cataloging of genes and features in organisms and comparing common features between organisms that associate with phenotypes.
2) Multiple pathogen and plant genomes have enabled studying epidemiology through tracing historical origins, emergence in new areas, and host jumps.
3) Genomics provides diagnostic tools for precise pathogen identification needed for quarantine and legislation.
Mingdong_research focus with references 2017.01Mingdong Huang
The document summarizes the author's recent research focusing on three directions: (1) studying the structures and functions of fibrinolytic proteins and developing inhibitors for them, (2) determining the structures of cell surface receptors and human serum albumin, and (3) developing a fluorescent probe for biomedical imaging, cancer therapy, and antimicrobial applications by conjugating it to targeting peptides. The author has determined several protein crystal structures and developed peptide inhibitors for proteases involved in cancer metastasis. The fluorescent probe conjugates show tumor targeting capability in mouse models and effectiveness against drug resistant bacteria.
This document provides a bibliography or list of references for the topic of "Identification and Validation of Drug Targets". It includes over 150 references in APA citation format from various sources like published papers, patents, books and reports. The references are grouped alphabetically and provide information to support further research on drug target identification and validation methods.
This article reports the detection of two gas clouds with no discernible elements heavier than hydrogen, representing the lowest heavy-element abundance observed in the early universe. One cloud at z=3.4 exhibits a deuterium abundance matching predictions from Big Bang nucleosynthesis, providing direct evidence for the standard cosmological model. The sparse metal enrichment of these clouds implies an inhomogeneous process for transporting heavy elements from galaxies into the surrounding intergalactic medium.
This curriculum vitae summarizes the academic and employment history, education, research activities, and publications of Joshua Harris Singer. Some key details include:
- Singer is currently an Associate Professor in the Department of Biology at the University of Maryland. He was previously an Assistant Professor at Northwestern University and UMD.
- He received a ScB in Biology from Brown University and a PhD in Physiology from the University of Washington.
- His research focuses on synaptic transmission and retinal circuit function, as evidenced by over 25 peer-reviewed publications on these topics. He has also given numerous invited talks on his research.
CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis...Surya Saha
CitrusCyc is a metabolic pathway database for the Citrus clementina and Citrus sinensis genomes. It was constructed using the Pathway Tools software and contains pathways, reactions, enzymes and genes derived from the annotated citrus genomes and the MetaCyc database. The database contains over 25,000 proteins and 40,000 transcripts with EC numbers for both citrus species. It provides visualizations of metabolic pathways and allows for overlay of RNA-seq expression data. Future work includes manual curation of pathways and development of a Meta-CitrusCyc database.
Ensuring Chemical Structure, Biological Data and Computational Model Quality
A talk given at SLAS 2016 mon Jan 25th in San Diego
covers published work and recent forays with BIA 10-2474
Maternal curcumin exposure causes fetal gross morphological anomalies and ske...Innspub Net
Curcumin is a phenolic compound extracted from the rhizome of turmeric (Curcuma longa L.). Although declared as safe for human consumption, curcumin has been found to be embryotoxic in some organisms indicating its potential as a teratogen. In this study, the teratogenic effect of maternal curcumin exposure in mouse fetuses was evaluated. Three experimental groups of pregnant mice were treated with 1.05, 1.52, and 2.0 mg/g body weight/day 95% curcumin, respectively, from gestation day (GD) 6 to 15. A fourth group without curcumin exposure served as a control. At GD18, the mice were sacrificed and the total number of implanted embryos including resorbed, dead, and live fetuses were counted for litter analysis. Extracted fetuses were also analyzed for gross morphological anomalies and subsequently have undergone alizarin staining for the visualization of skeletal malformations. Results showed an increased resorption rate in the 2.0 mg/g treatment (p<0.001). There is also a reduction of fetal weight (p<0.001) and crown-rump length (p<0.001) in a dose-dependent manner. Gross morphological analysis shows cranio-facial malformations such as flattened nose bridge (p<0.05) and micrognathia (p<0.05) in 2.0 mg/g treatment. Skeletal malformations such as large anterior fontanelle (p<0.001), misaligned ossification centers in the sternum (p<0.001), and delayed ossification in the forepaws, hind paws, and caudal vertebrae (p<0.001) were also observed at 2.0 mg/g treatment. Meanwhile, the presence of supernumerary ribs is not statistically different in the four groups. The results indicate that curcumin is teratogenic in mouse fetuses due to observed gross morphological anomalies and skeletal malformations.
Kelvin Yaprianto is a biochemist from Indonesia who received his Bachelor of Science with Honours degree from the Walter and Eliza Hall Institute of Medical Research in Australia in 2013. He has extensive research experience investigating the roles of NF-κB family transcription factors in promoting tumor cell survival and metastasis. Currently he works as a research assistant in stem cell and cancer research at PT. Kalbe Farma Tbk. in Jakarta.
Using Long Reads, Optical Maps and Long-Range Scaffolding to improve the Diap...Surya Saha
The document discusses efforts to improve the genome assembly of the Asian citrus psyllid (Diaphorina citri), the insect vector of citrus greening disease. It describes using long read sequencing data from PacBio to generate a new assembly with an N50 of 83kb, a significant improvement over the previous N50 of 34kb. It further discusses additional efforts using technologies like Dovetail scaffolding, 10X Genomics, and optical mapping to further improve scaffolding and resolve haplotypes, with the goal of generating a high-quality reference genome for D. citri.
This study investigated the use of noninvasive neuromodulation strategies to reactivate motor control in individuals with complete paralysis. Specifically, it used transcutaneous electrical stimulation of the spinal cord combined with passive limb movements and pharmacological intervention to facilitate voluntary locomotor-like movements. Over 18 weeks of weekly training, all 5 subjects showed improvements in their ability to generate stepping movements, both with and without stimulation. Electrophysiological data provided evidence that connectivity between the brain and spinal cord was reestablished. The combined noninvasive strategies were able to transform dormant neural networks into functional systems capable of voluntary movement recovery after complete paralysis.
How the artificial intelligence tool iPGK-PseAAC is working in predicting lys...IJBNT Journal
In 2017 a very powerful AI (artificial intelligence) tool
has been established for predicting lysine phosphoglycerylation sites in proteins, one of the most important post
modifications in proteins
The pLoc bal-mHum is a powerful web-serve for predicting the subcellular loca...IJBNT Journal
This document describes a powerful web server called pLoc bal-mHum that was developed in 2019 to predict the subcellular localization of human proteins based solely on their amino acid sequences. The tool uses artificial intelligence/machine learning techniques and was shown to predict localization with 94-100% accuracy across 14 different subcellular locations. The tool follows Chou's 5-step rule for developing predictive models in a logical, transparent, and reproducible manner. It has been widely cited and used by other researchers for developing predictive models of post-translational modifications and subcellular locations of proteins from various organisms.
ZEN 362 assignment: Effects of disasters. In this presentation we looked at a study conducted by Yamashiro et al. (2013) about the effects of radioactive caesium on bull testes after the Fukushima nuclear plant accident.
This curriculum vitae summarizes the educational and professional experience of Dr. Wen-Hai Chou. He received his PhD from the University of Texas Health Science Center in 2000 and is currently an Assistant Professor at Kent State University. His research focuses on the roles of Protein Kinase C and Lipocalin-2 in stroke. He has over 10 peer-reviewed publications in high impact journals such as the Journal of Neuroscience and Journal of Biological Chemistry.
Adarsh Jose is a PhD candidate in Bioinformatics and Computational Biology at Iowa State University. His research focuses on analyzing next-generation sequencing data to study gene expression, metabolic pathways, and protein interactions in various organisms. He has developed software for functional annotation and ortholog prediction from transcriptomes. Jose has presented his work at several conferences and collaborates with researchers studying hydrocarbon synthesis in microbes and plants.
In an era of increasing human longevity, it is becoming ever more critical to prioritize no only improved treatment of disease but also approaches for maintaining wellness to preserve the quality of life for aging adults. Spaceflight-induced physiological changes represent deviations from this state of wellness, with some changes serving as accelerated models of Earth-based conditions, including musculoskeletal disease, immune dysfunction, and delayed wound healing. This session will highlight research onboard the ISS National Lab that seeks to exploit these spaceflight-induced physiological effects to improve human health on Earth through studies that advance the prevention, detection, and treatment of disease. In parallel, spaceflight research and development efforts also seek to improve the human condition by employing the space environment to advance diagnostic tools and drug discovery, development and delivery systems.
Urmi Roy, Biochemistry, Clarkson University, Potsdam, NYUrmi Roy
This document provides a curriculum vitae for Urmi Roy, including her contact information, education history, research interests, publications, presentations, and affiliations. She received her Ph.D. in 2002 from the Indian Institute of Chemical Biology, specializing in nuclear medicine and drug design. Her current research focuses on structural biology, protein chemistry, and computational modeling to explore applications for drug discovery. She has over 20 publications and has presented her work at several conferences. She is currently an Adjunct Research Associate Professor at Clarkson University.
This document summarizes a study examining the formation and function of the contractile ring involved in polar body extrusion in the surf clam Spisula. The study found that:
1) The metaphase peripheral aster spreads along the egg cortex in an umbrella-like pattern, leaving a microtubule-poor center.
2) During anaphase, the aster disassembles as a cortical F-actin ring forms that matches the location, size, and pattern of the previous aster.
3) Inhibiting F-actin or myosin blocked polar body formation, while disrupting or stabilizing asters prevented proper ring and polar body formation, supporting the hypothesis that aster spreading
This document appears to be an email from Pearl Jacobson, a science librarian at Carleton University, to Ian Gordon. The email contains a citation for a research article from Inorganic Chemistry exploring the coordination chemistry of a bipyridine ligand. The citation includes the authors, title, journal, year, volume, issue pages and DOI for the research article.
This study characterized microstructural mutation events (MMEs) in chloroplast genomes of nine chloridoid grass species. High-throughput sequencing was used to obtain complete chloroplast genomes, which were aligned and analyzed for indels and inversions. Phylogenomic analyses of nucleotide sequences and binary matrices of MMEs produced trees with varying levels of support. MMEs provided additional phylogenetic information beyond nucleotide substitutions alone. The analysis of complete chloroplast genomes and MMEs improves understanding of evolutionary relationships among C4 chloridoid grasses.
Sense and Similarity: making sense of similarity for ontologiesCatia Pesquita
My keynote at the 20th BioOntologies meeting at ISMB/ECCB 2017. It focuses on discussing the challenges and opportunities of ontology semantic similarity and ontology matching to support semantic interoperability.
This document provides a resume for Kirsten Anice Messick. It summarizes her experience as a senior supervisor with over 11 years of experience in the pharmaceutical industry, supervising pre-clinical studies. She has extensive experience conducting in-vivo studies, developing protocols, and training others. She received a Bachelor's degree in Pharmacology and Immunology from Monash University in Australia and holds several certifications related to laboratory animal handling and veterinary assisting. Her roles at Genentech included supervising research associates, scheduling studies, developing animal models, and writing preclinical protocols.
This document summarizes research characterizing the CRISPR-Cas adaptive immune system in the archaeon DS1. The aims were to: 1) Characterize CRISPR-associated and unassociated genes, 2) Classify the system based on recent criteria (Type I, II, or III), and 3) Identify potential viruses from spacer sequences. The system was found to be an atypical Type IIIB-like system containing Type I adaptation proteins. CRISPR arrays were present without associated genes. Spacer sequences did not match other scaffolds, suggesting interference with unknown elements. The system may control gene expression through RNA-targeting proteins rather than targeting DNA viruses.
This document describes a new technique for wide-field background-free fluorescence imaging in vivo using magnetic modulation of fluorescent nanodiamond emission. Fluorescent nanodiamonds are promising probes for in vivo imaging but are limited by autofluorescence. The technique uses a rotating magnetic field to selectively modulate nanodiamond fluorescence, which is then detected using phase-sensitive lock-in detection to improve signal-to-background ratio up to 100-fold. This overcomes autofluorescence and improves nanodiamond imaging capabilities for in vivo applications.
Molecular Biologist Academic CV for Industry or Private Sector Consideration Sirie Godshalk
Molecular Biologist with over thirteen years of hands-on research experience, impactful writer and presenter, dynamic leader and enthusiastic team player with an eye for great ideas and a passion to move science in new directions seeks challenging opportunities beyond the bench.
Science and technology are essential to national development and progress. The government will prioritize research and development to support industries and improve life. It will also support local scientific capabilities and integrate technology into the economy. The government provides incentives for private sector participation in research and gives assistance to science students and researchers. It regulates foreign technology transfer and promotes community participation in generating and applying science and technology. Inventors' intellectual property is protected for periods defined by law. The Department of Science and Technology leads the country's science and technology efforts by setting policies, programs, and projects to support development through partnerships, applied research, acquiring technology, developing expertise, and strengthening international collaboration.
The document discusses Article 14 of the Indian Constitution which guarantees equality before the law and equal protection of laws. It explains that Article 14 prohibits unreasonable discrimination and establishes equality of status and opportunity. While equality before law means absence of special privileges, equal protection of laws ensures equal treatment in equal circumstances. The article elaborates on the principles of equality before law, equal protection of laws, and reasonable classification and discusses Supreme Court rulings regarding Article 14.
Ensuring Chemical Structure, Biological Data and Computational Model Quality
A talk given at SLAS 2016 mon Jan 25th in San Diego
covers published work and recent forays with BIA 10-2474
Maternal curcumin exposure causes fetal gross morphological anomalies and ske...Innspub Net
Curcumin is a phenolic compound extracted from the rhizome of turmeric (Curcuma longa L.). Although declared as safe for human consumption, curcumin has been found to be embryotoxic in some organisms indicating its potential as a teratogen. In this study, the teratogenic effect of maternal curcumin exposure in mouse fetuses was evaluated. Three experimental groups of pregnant mice were treated with 1.05, 1.52, and 2.0 mg/g body weight/day 95% curcumin, respectively, from gestation day (GD) 6 to 15. A fourth group without curcumin exposure served as a control. At GD18, the mice were sacrificed and the total number of implanted embryos including resorbed, dead, and live fetuses were counted for litter analysis. Extracted fetuses were also analyzed for gross morphological anomalies and subsequently have undergone alizarin staining for the visualization of skeletal malformations. Results showed an increased resorption rate in the 2.0 mg/g treatment (p<0.001). There is also a reduction of fetal weight (p<0.001) and crown-rump length (p<0.001) in a dose-dependent manner. Gross morphological analysis shows cranio-facial malformations such as flattened nose bridge (p<0.05) and micrognathia (p<0.05) in 2.0 mg/g treatment. Skeletal malformations such as large anterior fontanelle (p<0.001), misaligned ossification centers in the sternum (p<0.001), and delayed ossification in the forepaws, hind paws, and caudal vertebrae (p<0.001) were also observed at 2.0 mg/g treatment. Meanwhile, the presence of supernumerary ribs is not statistically different in the four groups. The results indicate that curcumin is teratogenic in mouse fetuses due to observed gross morphological anomalies and skeletal malformations.
Kelvin Yaprianto is a biochemist from Indonesia who received his Bachelor of Science with Honours degree from the Walter and Eliza Hall Institute of Medical Research in Australia in 2013. He has extensive research experience investigating the roles of NF-κB family transcription factors in promoting tumor cell survival and metastasis. Currently he works as a research assistant in stem cell and cancer research at PT. Kalbe Farma Tbk. in Jakarta.
Using Long Reads, Optical Maps and Long-Range Scaffolding to improve the Diap...Surya Saha
The document discusses efforts to improve the genome assembly of the Asian citrus psyllid (Diaphorina citri), the insect vector of citrus greening disease. It describes using long read sequencing data from PacBio to generate a new assembly with an N50 of 83kb, a significant improvement over the previous N50 of 34kb. It further discusses additional efforts using technologies like Dovetail scaffolding, 10X Genomics, and optical mapping to further improve scaffolding and resolve haplotypes, with the goal of generating a high-quality reference genome for D. citri.
This study investigated the use of noninvasive neuromodulation strategies to reactivate motor control in individuals with complete paralysis. Specifically, it used transcutaneous electrical stimulation of the spinal cord combined with passive limb movements and pharmacological intervention to facilitate voluntary locomotor-like movements. Over 18 weeks of weekly training, all 5 subjects showed improvements in their ability to generate stepping movements, both with and without stimulation. Electrophysiological data provided evidence that connectivity between the brain and spinal cord was reestablished. The combined noninvasive strategies were able to transform dormant neural networks into functional systems capable of voluntary movement recovery after complete paralysis.
How the artificial intelligence tool iPGK-PseAAC is working in predicting lys...IJBNT Journal
In 2017 a very powerful AI (artificial intelligence) tool
has been established for predicting lysine phosphoglycerylation sites in proteins, one of the most important post
modifications in proteins
The pLoc bal-mHum is a powerful web-serve for predicting the subcellular loca...IJBNT Journal
This document describes a powerful web server called pLoc bal-mHum that was developed in 2019 to predict the subcellular localization of human proteins based solely on their amino acid sequences. The tool uses artificial intelligence/machine learning techniques and was shown to predict localization with 94-100% accuracy across 14 different subcellular locations. The tool follows Chou's 5-step rule for developing predictive models in a logical, transparent, and reproducible manner. It has been widely cited and used by other researchers for developing predictive models of post-translational modifications and subcellular locations of proteins from various organisms.
ZEN 362 assignment: Effects of disasters. In this presentation we looked at a study conducted by Yamashiro et al. (2013) about the effects of radioactive caesium on bull testes after the Fukushima nuclear plant accident.
This curriculum vitae summarizes the educational and professional experience of Dr. Wen-Hai Chou. He received his PhD from the University of Texas Health Science Center in 2000 and is currently an Assistant Professor at Kent State University. His research focuses on the roles of Protein Kinase C and Lipocalin-2 in stroke. He has over 10 peer-reviewed publications in high impact journals such as the Journal of Neuroscience and Journal of Biological Chemistry.
Adarsh Jose is a PhD candidate in Bioinformatics and Computational Biology at Iowa State University. His research focuses on analyzing next-generation sequencing data to study gene expression, metabolic pathways, and protein interactions in various organisms. He has developed software for functional annotation and ortholog prediction from transcriptomes. Jose has presented his work at several conferences and collaborates with researchers studying hydrocarbon synthesis in microbes and plants.
In an era of increasing human longevity, it is becoming ever more critical to prioritize no only improved treatment of disease but also approaches for maintaining wellness to preserve the quality of life for aging adults. Spaceflight-induced physiological changes represent deviations from this state of wellness, with some changes serving as accelerated models of Earth-based conditions, including musculoskeletal disease, immune dysfunction, and delayed wound healing. This session will highlight research onboard the ISS National Lab that seeks to exploit these spaceflight-induced physiological effects to improve human health on Earth through studies that advance the prevention, detection, and treatment of disease. In parallel, spaceflight research and development efforts also seek to improve the human condition by employing the space environment to advance diagnostic tools and drug discovery, development and delivery systems.
Urmi Roy, Biochemistry, Clarkson University, Potsdam, NYUrmi Roy
This document provides a curriculum vitae for Urmi Roy, including her contact information, education history, research interests, publications, presentations, and affiliations. She received her Ph.D. in 2002 from the Indian Institute of Chemical Biology, specializing in nuclear medicine and drug design. Her current research focuses on structural biology, protein chemistry, and computational modeling to explore applications for drug discovery. She has over 20 publications and has presented her work at several conferences. She is currently an Adjunct Research Associate Professor at Clarkson University.
This document summarizes a study examining the formation and function of the contractile ring involved in polar body extrusion in the surf clam Spisula. The study found that:
1) The metaphase peripheral aster spreads along the egg cortex in an umbrella-like pattern, leaving a microtubule-poor center.
2) During anaphase, the aster disassembles as a cortical F-actin ring forms that matches the location, size, and pattern of the previous aster.
3) Inhibiting F-actin or myosin blocked polar body formation, while disrupting or stabilizing asters prevented proper ring and polar body formation, supporting the hypothesis that aster spreading
This document appears to be an email from Pearl Jacobson, a science librarian at Carleton University, to Ian Gordon. The email contains a citation for a research article from Inorganic Chemistry exploring the coordination chemistry of a bipyridine ligand. The citation includes the authors, title, journal, year, volume, issue pages and DOI for the research article.
This study characterized microstructural mutation events (MMEs) in chloroplast genomes of nine chloridoid grass species. High-throughput sequencing was used to obtain complete chloroplast genomes, which were aligned and analyzed for indels and inversions. Phylogenomic analyses of nucleotide sequences and binary matrices of MMEs produced trees with varying levels of support. MMEs provided additional phylogenetic information beyond nucleotide substitutions alone. The analysis of complete chloroplast genomes and MMEs improves understanding of evolutionary relationships among C4 chloridoid grasses.
Sense and Similarity: making sense of similarity for ontologiesCatia Pesquita
My keynote at the 20th BioOntologies meeting at ISMB/ECCB 2017. It focuses on discussing the challenges and opportunities of ontology semantic similarity and ontology matching to support semantic interoperability.
This document provides a resume for Kirsten Anice Messick. It summarizes her experience as a senior supervisor with over 11 years of experience in the pharmaceutical industry, supervising pre-clinical studies. She has extensive experience conducting in-vivo studies, developing protocols, and training others. She received a Bachelor's degree in Pharmacology and Immunology from Monash University in Australia and holds several certifications related to laboratory animal handling and veterinary assisting. Her roles at Genentech included supervising research associates, scheduling studies, developing animal models, and writing preclinical protocols.
This document summarizes research characterizing the CRISPR-Cas adaptive immune system in the archaeon DS1. The aims were to: 1) Characterize CRISPR-associated and unassociated genes, 2) Classify the system based on recent criteria (Type I, II, or III), and 3) Identify potential viruses from spacer sequences. The system was found to be an atypical Type IIIB-like system containing Type I adaptation proteins. CRISPR arrays were present without associated genes. Spacer sequences did not match other scaffolds, suggesting interference with unknown elements. The system may control gene expression through RNA-targeting proteins rather than targeting DNA viruses.
This document describes a new technique for wide-field background-free fluorescence imaging in vivo using magnetic modulation of fluorescent nanodiamond emission. Fluorescent nanodiamonds are promising probes for in vivo imaging but are limited by autofluorescence. The technique uses a rotating magnetic field to selectively modulate nanodiamond fluorescence, which is then detected using phase-sensitive lock-in detection to improve signal-to-background ratio up to 100-fold. This overcomes autofluorescence and improves nanodiamond imaging capabilities for in vivo applications.
Molecular Biologist Academic CV for Industry or Private Sector Consideration Sirie Godshalk
Molecular Biologist with over thirteen years of hands-on research experience, impactful writer and presenter, dynamic leader and enthusiastic team player with an eye for great ideas and a passion to move science in new directions seeks challenging opportunities beyond the bench.
Science and technology are essential to national development and progress. The government will prioritize research and development to support industries and improve life. It will also support local scientific capabilities and integrate technology into the economy. The government provides incentives for private sector participation in research and gives assistance to science students and researchers. It regulates foreign technology transfer and promotes community participation in generating and applying science and technology. Inventors' intellectual property is protected for periods defined by law. The Department of Science and Technology leads the country's science and technology efforts by setting policies, programs, and projects to support development through partnerships, applied research, acquiring technology, developing expertise, and strengthening international collaboration.
The document discusses Article 14 of the Indian Constitution which guarantees equality before the law and equal protection of laws. It explains that Article 14 prohibits unreasonable discrimination and establishes equality of status and opportunity. While equality before law means absence of special privileges, equal protection of laws ensures equal treatment in equal circumstances. The article elaborates on the principles of equality before law, equal protection of laws, and reasonable classification and discusses Supreme Court rulings regarding Article 14.
Article 14 Education, Science and Technology, Arts,Culture and SportsCherie Ann
This document contains the provisions for education, science and technology, arts, culture and sports in the Philippines constitution. It establishes the right to quality education for all citizens and mandates a complete education system from elementary to higher education. It also promotes the development and preservation of Filipino culture and heritage. The state is tasked with prioritizing research and innovation to support national development.
The Department of Education is the executive department of the Philippine government responsible for managing the country's basic education system. It oversees the primary and secondary school system and formulates educational policy. During the Spanish colonial period, education was primarily for the elite but was later liberalized and secularized through the 1863 Educational Decree. The Department of Education now aims to provide quality, equitable, and accessible basic education and lifelong learning.
The 1987 constitution of the republic of the philippines article xiv - educ...Jared Ram Juezan
This document outlines the key provisions for education, science and technology, arts, culture and sports according to the 1987 Constitution of the Republic of the Philippines. It establishes the state's role in protecting and promoting the right to quality education for all citizens. It also mandates a free public education system and sets guidelines for governance and funding of educational institutions. The document also addresses language policy, the development of science and technology, fostering arts and culture, and the promotion of sports.
The document outlines the principles of the Philippine constitution. It establishes that the Philippines is a democratic and republican state where sovereignty resides with the people. It discusses the country's adherence to democratic principles like separation of powers and free elections. It also covers foreign policy principles like renouncing war and adhering to international law. The constitution aims to protect civil liberties and promote social justice.
The gravity field_and_interior_structure_of_enceladusSérgio Sacani
The gravity field and interior structure of Enceladus were determined using Doppler data from three Cassini flybys. There is a negative mass anomaly in the south polar region, largely compensated by a positive subsurface anomaly consistent with a regional subsurface sea at depths of 30-40 km extending to 50° south latitude. Enceladus deviates mildly from hydrostatic equilibrium, with estimated quadrupole coefficients indicating a differentiated body with a low-density core.
The gravity fieldandinteriorstructureofenceladusGOASA
The Cassini spacecraft measured Enceladus' gravity field during three flybys. The results indicate a negative mass anomaly over the south pole, likely compensated by a subsurface sea of water 30-40 km deep extending to 50° south latitude. Analysis of the gravity data suggests Enceladus has differentiated into a low-density core with a moment of inertia around 0.335 times its mass times the square of its radius, consistent with the presence of liquid water beneath the surface. The endogenic heat output and gravity data are best explained by models involving tidal heating of Enceladus' interior through past or current orbital resonances.
Minor Planet Evidence for Water in the Rocky Debris of a Disrupted Extrasolar...Carlos Bella
Evidence has been found for water in the debris of a disrupted extrasolar minor planet orbiting a white dwarf star. Spectroscopic analysis of the white dwarf's atmosphere revealed an excess of oxygen that cannot be explained by oxide minerals alone, indicating the parent body was originally composed of about 26% water by mass. This demonstrates that water-bearing planetesimals can form around higher mass stars that eventually become white dwarfs. The disrupted planetesimal is the source of a circumstellar debris disk closely orbiting the white dwarf remnant.
This document describes research on depositing semiconductors and metals within the pores of microstructured optical fibers using high-pressure microfluidic chemical vapor deposition. Specifically, it demonstrates the fabrication of germanium nanotubes, coaxial heterojunction structures, and longitudinally patterned structures within fiber pores. This integration of functional materials into optical fibers could enable new fiber-integrated optoelectronic devices and materials.
1. Researchers injected mice with a virus that causes neurons activated during exploration of a novel context to express channelrhodopsin-2 (ChR2). They labeled dentate gyrus neurons activated during exploration of context A with ChR2.
2. On a later day, they optically stimulated the neurons labeled in context A while delivering a foot shock in a different context B, to test if this could generate a false fear memory for context A.
3. When later tested, mice that received optical stimulation of dentate gyrus neurons showed increased freezing in context A, where no shock was delivered, demonstrating the creation of a false fear memory through artificial means.
Measurements of energetic_particle_radiation_in_transit_to_mars_on_the_mars_s...Sérgio Sacani
The Radiation Assessment Detector on the Mars Science Laboratory measured the radiation environment inside the spacecraft during its 253-day cruise to Mars. It found a galactic cosmic ray dose rate of 332 mGy/day in silicon or 481 mGy/day in water. The quality factor for the radiation field was 3.82, indicating it was more biologically damaging than an equal dose of low-LET radiation. Integrating the measured energy and linear energy transfer spectra against quality factors yielded a total mission dose equivalent of 0.66 sievert for the round-trip cruise, posing health risks for future human Mars missions with current propulsion technologies and shielding.
The document reports measurements of isotope ratios in CO2 and H2O in the Martian atmosphere taken by the Curiosity rover. Isotope ratios of hydrogen, carbon, and oxygen can reveal information about planetary processes like atmospheric loss and interactions with the surface. The measurements imply that the Martian reservoirs of CO2 and H2O were largely established 4 billion years ago, but that some atmospheric loss or surface interaction may still be ongoing. Comparison to measurements of Martian meteorites provides information about these long-term planetary processes and the evolution of the Martian atmosphere and surface.
A population of_fast_radio_bursts_ar_cosmological_distancesSérgio Sacani
1) Four fast radio bursts (FRBs) lasting only a few milliseconds were detected in a radio survey of the high Galactic latitude sky.
2) The bursts' properties indicate they are of celestial rather than terrestrial origin and likely originate from cosmological distances of 0.5 to 3 billion light years.
3) No coincident x-ray or gamma-ray signals were found associated with the bursts. Characterizing the population of FRBs could help determine the baryonic content of the universe.
Multi-molecular views of a stellar nurserySérgio Sacani
New detectors for radio telescopes can map emissions from many different molecules simultaneously across interstellar clouds. One such pioneering study has probed a wide area of a star-forming cloud in the Orion constellation
The document reports on a study investigating the role of the p38 mitogen-activated protein kinase p38γ in Alzheimer's disease (AD) pathogenesis. The study found that depletion of p38γ exacerbated neuronal excitotoxicity, cognitive deficits, neuronal circuit abnormalities, and premature mortality in an AD mouse model overexpressing amyloid-β (Aβ). In contrast, increasing p38γ activity abolished these Aβ-induced deficits. Furthermore, mimicking site-specific tau phosphorylation by p38γ alleviated Aβ-induced neuronal death and excitotoxicity. The findings suggest p38γ phosphorylation of tau at specific sites inhibits Aβ toxicity in early AD, challenging the view that tau phosphorylation is purely pathogenic.
"Keeping up with the plant destroyers." My talk at The Royal Society, 7 March...Sophien Kamoun
Tackling emerging threats to animal health, food security and ecosystem resilience, The Royal Society, Monday 7 – Tuesday 8 March 2016. https://royalsociety.org/events/2016/03/emerging-fungal-threats/
This document summarizes a scientific paper published in Science in 2011 about the discovery that the large, oxygen-rich halos surrounding star-forming galaxies are a major reservoir of heavy elements ejected from galaxies. The paper presents evidence that these halos contain a significant portion of metals produced by massive stars. It also describes how these findings help scientists better understand the cycling of matter on large scales throughout the universe.
Systems Biology & Pharmacology from a Structural PerspectivePhilip Bourne
Philip Bourne gave a talk on his past research leading data science at the NIH and his current and future research. Some of his past work includes developing methods for determining binding site similarity across protein space using geometric potentials and sequence-order independent profile-profile alignment. His current research focuses on using these methods for applications like predicting drug efficacy, toxicity and repurposing old drugs for new uses. He discussed challenges like the large search space and flexibility of proteins. Going forward, he hopes cloud computing environments can help make data and tools more accessible and reusable to advance systems pharmacology research.
- Comet C/2011 N3 (SOHO) was observed by the Solar Dynamics Observatory as it passed through the low solar corona in July 2011.
- The comet survived within the corona until it came within 0.146 solar radii (approximately 100,000 km) of the solar surface, at which point its extreme ultraviolet signal disappeared.
- Before being destroyed, material released from the comet was first seen in absorption against the solar corona, then formed an emission nebula as it interacted with the coronal plasma.
The absolute chronology and thermal processing of solids in the solar protopl...Carlos Bella
CAIs define a brief formation interval corresponding to an age of 4567.30 ± 0.16 million years, whereas chondrules range from 4567.32 ± 0.42 to 4564.71 ± 0.30 million years. U-Pb dating refutes the long-held view of an age gap between CAIs and chondrules, instead indicating chondrule formation started contemporaneously with CAIs and lasted ~3 million years. This timeline is similar to protoplanetary disk lifetimes from astronomy, suggesting CAI and chondrule formation occurred during the evolution of the solar protoplanetary disk.
The study compared the stimulus generalization patterns of increases and decreases in vestibuloocular reflex (VOR) gain that were induced through motor learning in mice and monkeys. Decreases in VOR gain were found to generalize more across different frequencies of head rotation than increases in gain, as seen in both the gain and phase of the VOR response. This difference held even when animals were trained with high-frequency stimuli, suggesting that increases and decreases in VOR gain are not exact inverses at the circuit level. Plasticity mechanisms supporting decreases in gain must affect neurons more broadly tuned for head rotation frequency than mechanisms for increases in gain.
a
PATTERNS & PHENOTYPES
A Novel Planar Polarity Gene Pepsinogen-Like Regulates
Wingless Expression in a Posttranscriptional Manner
Kousuke Mouri,1 Yutaro Nishino,1 Masaki Arata,1 Dongbo Shi,1 Shin-Ya Horiuchi,1 and Tadashi Uemura1,2*
1Graduate School of Biostudies, Kyoto University, Kyoto, Japan
2
CREST, Japan Science and Technology Agency, Saitama, Japan
Background: Planar cell polarity (PCP) originally referred to the coordination of global organ axes and individual cell polarity
within the plane of the epithelium. More recently, it has been accepted that pertinent PCP regulators play essential roles not
only in epithelial sheets, but also in various rearranging cells. Results: We identified pepsinogen-like (pcl) as a new planar polarity
gene, using Drosophila wing epidermis as a model. Pcl protein is predicted to belong to a family of aspartic proteases. When pcl
mutant clones were observed in pupal wings, PCP was disturbed in both mutant and wild-type cells that were juxtaposed to the
clone border. We examined levels of known PCP proteins in wing imaginal discs. The amount of the seven-pass transmembrane
cadherin Flamingo (Fmi), one of the PCP “core group” members, was significantly decreased in mutant clones, whereas neither
the amount of nor the polarized localization of Dachsous (Ds) at cell boundaries was affected. In addition to the PCP phenotype,
the pcl mutation caused loss of wing margins. Intriguingly, this was most likely due to a dramatic decrease in the level of Wing-
less (Wg) protein, but not due to a decrease in the level of wg transcripts. Conclusions: Our results raise the possibility that
Pcl regulates Wg expression post-transcriptionally, and PCP, by proteolytic cleavages. Developmental Dynamics 243:791–799,
2014. VC 2014 Wiley Periodicals, Inc.
Key words: aspartic protease; Wnt signaling pathway; planar cell polarity; Drosophila melanogaster
Submitted 27 September 2013; First Decision 28 December 2013; Accepted 28 December 2013; Published online 8 January 2014
Introduction
In epithelia, cells are polarized along a fixed axis within the plane,
which is critical for many organ functions. Underlying mecha-
nisms of this planar cell polarity (PCP) have been best studied in
the Drosophila wing, where epidermal cells somehow sense an
organ axis, localize an assembly of actin filaments at the distal cell
vertexes, and produce single wing hairs in pupae (Adler, 2002). It
has been shown that evolutionary conserved regulators of PCP
orchestrate a variety of collective cell behaviors, such as polarized
protrusive cell activity, directional cell movement, and oriented
cell division, so they are crucial for the normal development of
both epithelial and non-epithelial tissues (Seifert and Mlodzik,
2007; Gray et al., 2011; Vichas and Zallen, 2011).
In spite of a number of molecular players identified, a long-
standing question is how exactly individual cell polarity is coordi-
nated with global organ axes. At the molecular l.
An accurate distance_to_the_nearest_galaxySérgio Sacani
This document summarizes recent research that more accurately measured the distance to the Large Magellanic Cloud (LMC) galaxy. A team called the Araucaria Project measured the distances to eight eclipsing binary stars in the LMC to determine a distance of 49.3 ± 0.5 kiloparsecs, which is accurate to 2.2%. This more precise measurement of the distance to the LMC will help astronomers better determine distances to more distant galaxies and improve our understanding of properties like dark energy. The new measurement is consistent with but more accurate than previous estimates, addressing issues with prior discrepancies in LMC distance measurements.
This document summarizes epigenetics quality control (EpiQC) efforts for several reference epigenome samples, including various epigenetic assays and datasets that have been or will be generated. It discusses completed whole-genome bisulfite sequencing, methylation array, and single molecule real-time sequencing data for several samples, as well as planned additional assays including oxidative bisulfite sequencing and single-cell reduced representation bisulfite sequencing. The goal is to establish high-quality reference epigenomes for use in assay development and validation through a collaborative consortium.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Anti-Universe And Emergent Gravity and the Dark UniverseSérgio Sacani
Recent theoretical progress indicates that spacetime and gravity emerge together from the entanglement structure of an underlying microscopic theory. These ideas are best understood in Anti-de Sitter space, where they rely on the area law for entanglement entropy. The extension to de Sitter space requires taking into account the entropy and temperature associated with the cosmological horizon. Using insights from string theory, black hole physics and quantum information theory we argue that the positive dark energy leads to a thermal volume law contribution to the entropy that overtakes the area law precisely at the cosmological horizon. Due to the competition between area and volume law entanglement the microscopic de Sitter states do not thermalise at sub-Hubble scales: they exhibit memory effects in the form of an entropy displacement caused by matter. The emergent laws of gravity contain an additional ‘dark’ gravitational force describing the ‘elastic’ response due to the entropy displacement. We derive an estimate of the strength of this extra force in terms of the baryonic mass, Newton’s constant and the Hubble acceleration scale a0 = cH0, and provide evidence for the fact that this additional ‘dark gravity force’ explains the observed phenomena in galaxies and clusters currently attributed to dark matter.
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDSSérgio Sacani
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 M⊙) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10−4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
PPT on Alternate Wetting and Drying presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
Evidence of Jet Activity from the Secondary Black Hole in the OJ 287 Binary S...Sérgio Sacani
Wereport the study of a huge optical intraday flare on 2021 November 12 at 2 a.m. UT in the blazar OJ287. In the binary black hole model, it is associated with an impact of the secondary black hole on the accretion disk of the primary. Our multifrequency observing campaign was set up to search for such a signature of the impact based on a prediction made 8 yr earlier. The first I-band results of the flare have already been reported by Kishore et al. (2024). Here we combine these data with our monitoring in the R-band. There is a big change in the R–I spectral index by 1.0 ±0.1 between the normal background and the flare, suggesting a new component of radiation. The polarization variation during the rise of the flare suggests the same. The limits on the source size place it most reasonably in the jet of the secondary BH. We then ask why we have not seen this phenomenon before. We show that OJ287 was never before observed with sufficient sensitivity on the night when the flare should have happened according to the binary model. We also study the probability that this flare is just an oversized example of intraday variability using the Krakow data set of intense monitoring between 2015 and 2023. We find that the occurrence of a flare of this size and rapidity is unlikely. In machine-readable Tables 1 and 2, we give the full orbit-linked historical light curve of OJ287 as well as the dense monitoring sample of Krakow.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
1. DOI: 10.1126/science.1242247
, 1490 (2013);342Science
et al.H. Murakawa
Detection of Berry's Phase in a Bulk Rashba Semiconductor
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Acknowledgments: We thank Y. Cheng and X. Li for providing
raw frame alignment scripts prior to publication, R. Henderson
for making the makestack_HRnoise.exe program available
for use to assess the overfitting of the EM data, J. Korzun for
technical assistance, J.-C. Ducom (TSRI) for support with
computational resources, and C. R. King and W. Koff for
support and encouragement. Supported by NIH grants HIVRAD
P01 AI82362 (J.P.M., I.A.W., and A.B.W.) and R01 AI36082
(I.A.W.); the International AIDS Vaccine Initiative Neutralizing
Antibody Consortium (D.R.B., J.P.M., I.A.W., A.B.W.); Scripps
CHAVI-ID (UM1 AI100663) (D.R.B., I.A.W., A.B.W.); a Vidi
grant from the Netherlands Organization for Scientific
Research (R.W.S.); a Starting Investigator Grant from the
European Research Council (R.W.S.); and a Canadian Institutes
of Health Research fellowship (J.-P.J.). The EM work was
conducted at the National Resource for Automated Molecular
Microscopy at The Scripps Research Institute, which is
supported by the Biomedical Technology Research Center
program (GM103310) of the National Institute of General
Medical Sciences (B.C., C.S.P.). 3D visualizations were
generated using the UCSF Chimera package. The EM
reconstructions have been deposited in the Electron Microscopy
Data Bank under accession codes EMD-5779, EMD-5780,
EMD-5781, and EMD-5782. The structure coordinates have
been deposited in the Protein Data Bank under accession code
3J5M. Sharing of other materials will be subject to standard
material transfer agreements. Raw EM data will be provided
upon request. The content is the responsibility of the authors
and does not necessarily reflect the official views of NIGMS or
NIH. IAVI has previously filed a patent relating to the BG505
SOSIP.664 trimer: U.S. Prov. Appln. No. 61/772,739, titled
“HIV-1 envelope glycoprotein,” with inventors M. Caulfield,
A.C., H. Dean, S. Hoffenberg, C. R. King, P.-J.K., A. Marozsan,
J.P.M., R.W.S., A.B.W., I.A.W., and J.-P.J. This is manuscript
25060 from The Scripps Research Institute.
Supplementary Materials
www.sciencemag.org/342/6165/1484/suppl/DC1
Materials and Methods
Figs. S1 to S20
Movie S1
References (55–74)
6 September 2013; accepted 7 October 2013
Published online 31 October 2013;
10.1126/science.1245627
REPORTS
Detection of Berry’s Phase in a Bulk
Rashba Semiconductor
H. Murakawa,1
*† M. S. Bahramy,1,2
M. Tokunaga,3
Y. Kohama,3
C. Bell,4
Y. Kaneko,1
N. Nagaosa,1,2
H. Y. Hwang,1,4
Y. Tokura1,2
The motion of electrons in a solid has a profound effect on its topological properties and may result in a
nonzero Berry’s phase, a geometric quantum phase encoded in the system’s electronic wave function.
Despite its ubiquity, there are few experimental observations of Berry’s phase of bulk states. Here, we
report detection of a nontrivial p Berry’s phase in the bulk Rashba semiconductor BiTeI via analysis of the
Shubnikov–de Haas (SdH) effect. The extremely large Rashba splitting in this material enables the
separation of SdH oscillations, stemming from the spin-split inner and outer Fermi surfaces. For both
Fermi surfaces, we observe a systematic p-phase shift in SdH oscillations, consistent with the theoretically
predicted nontrivial p Berry’s phase in Rashba systems.
Quantum mechanical systems undergoing
adiabatic evolution on a closed path in pa-
rameter space acquire a geometrical phase
known as Berry’s phase, fB (1, 2). A number of
emergent phenomena—including the anomalous
(3) and quantum (4) Hall effects, charge pumping
(5), and topological insulating and superconduct-
ing phases (6)—are driven by a nontrivial (that is,
nonzero) fB. A nontrivial fB can, for example, be
realized for charge carriers that have k-space cy-
clotron orbits enclosing a Dirac point (7–10). In
general, any closed cyclotron orbit is quantized
under an external magnetic field B, according to
the Lifshitz-Onsager quantization rule
An
ℏ
eB
¼ 2p n þ
1
2
−
fB
2p
¼ 2pðn þ gÞ ð1Þ
Here An is the extremal cross-sectional area of the
Fermi surface (FS) related to the Landau level
(LL) n; g is defined as g ¼ 1
2 − fB
2p and can take
values from 0 to 1, depending on the value of
1
RIKENCenterforEmergentMatterScience(CenterforEmergent
Matter Science), Wako 351-0198, Japan. 2
Department of Ap-
plied Physics and Quantum Phase Electronics Center, University
of Tokyo, Tokyo 113-8656, Japan. 3
International MegaGauss
ScienceLaboratory,InstituteforSolidStatePhysics,TheUniversity
of Tokyo, Kashiwa 277-8581, Japan. 4
Stanford Institute for Ma-
terials and Energy Sciences, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA.
*Present address: Department of Physics, Graduate School
of Science, Osaka University, Osaka, Japan.
†Corresponding author. E-mail: murakawa-h@riken.jp
20 DECEMBER 2013 VOL 342 SCIENCE www.sciencemag.org1490
3. fB (7); ħ is Planck’s constant h divided by 2p;
and e is the elementary charge. The quantity g
can be experimentally accessed by analyzing
the LL fan diagram of Shubnikov–de Haas (SdH)
oscillations. A nontrivial Berry’s phase has been
observed in pseudo-spin Dirac systems such as
graphene (10), as well as elemental bismuth (11),
bulk SrMnBi2 (12), and, potentially, graphite
(13–15), although in that case the experimental
situation remains unresolved. Clear detection in
physical-spin Dirac systems such as topological
insulators has been complicated by large Zeeman
energy effects and bulk conduction (16–19).
Systems described by the Rashba Hamiltonian
also possess a Dirac point and provide an alter-
native path to realizing a nontrivial fB. The Dirac
point in this class of noncentrosymmetric systems
results from the crossing between energy bands
spin-split by the Rashba spin-obit Hamiltonian
HR ¼ l
ℏ e ⋅ðs  pÞ, where l is the Rashba param-
eter, e is the unit vector along which the system
breaks inversion symmetry (20), s is the spin, and
p is the momentum vector. Because of this inter-
action, the energy bands are linearly dispersed
around p = 0, and the resulting FS consists of two
pockets, an inner FS (IFS) and an outer FS (OFS).
For each FS, s is locked to be normal to p, there-
by forming a helical spin texture around the Dirac
point at p = 0. It has been predicted that in sys-
tems where both Rashba and Dresselhaus spin-
orbit interactions are present, both FSs obtain a
Berry’s phase expressed as FB ¼ l2
− b2
jl2
− b2
j
p, with
b corresponding to the Dresselhaus parameter
(21–23). Accordingly, in the case of pure Rashba
spin splitting (RSS) (b = 0), both inner and outer
FSs are expected to obtain a nontrivial p Berry’s
phase. Consequences of this Rashba coupling and
phase have been studied in two dimensions in
semiconductor heterostructures using weak anti-
localization (24), ensemble averaging in interfer-
ometers (25), commensurability oscillations (26),
and SdH oscillations (27, 28). Given the relatively
small RSS in these systems, the IFS and OFS have
similar areas, and the SdH oscillations show beat-
ing patterns that obscure the underlying oscillation
index structure.In addition, when the spin is aligned
to the external magnetic field by a larger Zeeman
energy, RSS disappears, and the Berry’s phase
takes on the trivial value.
Recently, a large RSS in a bulk material has
been found in the polar semiconductor BiTeI
(29–32). This material is composed of alternating
Bi, Te, and I atoms stacked along the hexagonal c
axis and is typically electron-doped by native de-
fects, as found in many chalcogenide semicon-
ductors. Because of the absence of inversion
symmetry and the strong polarity of the system,
accompanied by the strong spin-orbit interaction
of Bi, an extremely large RSS occurs around the
hexagonal face center of the Brillouin zone, re-
ferred to as the A point (30). Both angle-resolved
photoemission spectroscopy and optical spec-
troscopy (29, 31–34) reveal that the RSS in BiTeI
approaches 400 meV, with a Dirac point located
~110 meV above the conduction band minimum,
in good agreement with relativistic first-principles
calculations (30, 35).
Figure 1 shows the calculated band dispersion
around the A point (Fig. 1A) and a typical FS for
a Fermi level EF located slightly above the Dirac
point (Fig. 1B), corresponding to the samples mea-
sured here. The large RSS causes the ratio of the
extremal cross-sectional areas of the IFS and OFS
to be extremely large, diverging as EF approaches
the Dirac point. In terms of SdH experiments for
samples with finite electron mobility, this conve-
niently decouples the two sets of oscillations by
confining the IFS and OFS to the low- and high-
field regime, respectively. Moreover, the observed
giant RSS in BiTeI can dominate the Zeeman
effect, even in high magnetic fields. Therefore,
BiTeI is an ideal system for investigating the Berry’s
phase originating from the Rashba spin-split band.
Figure 2 shows the in-plane magnetoresistiv-
ity (rxx) of a BiTeI sample (sample A) up to 14 T
applied along the [001] c axis at 1.8 K. In this
sample, the low-field Hall mobility is ~300 cm2
/
V·s at 1.8 K. The Hall density (~4.0 × 1019
cm−3
)
would place EF slightly above the Dirac point. As
can be seen, the SdH oscillations stemming from
the IFS (4 T) and OFS (10 T) are well separated
from each other; thus, they can be separately
analyzed. Focusing first on the IFS, Fig. 3A shows
the SdH oscillations at various temperatures. Be-
cause the IFS extremal cross-sectional area (AIFS)
is so small, 3.4 Tis sufficient to reach the quantum
limit, where all electron states in the IFS are con-
densed into the lowest LL. This can be seen by
taking the negative second derivative of resistivity
(–d2
rxx/dB2
) (Fig. 3B). Here, the lowest-index
maximum (corresponding to the peak in resistiv-
ity) appears at 3.4 T (1/B = 0.294 T–1
), and the
oscillation disappears above 5 T. The period of
the oscillation [∆(1/B) = 0.294 T–1
] corresponds to
AIFS = 3.1 × 10−4
Å−2
.
The oscillatory component ∆rxx is plotted in
Fig. 3C, after subtraction of the nonoscillating
background deduced by fitting a fourth-order
polynomial, based on the resistivity values at the
node positions of the SdH oscillations (Fig. 3A).
From the temperature dependence of the oscillation
amplitude at 3.4 T (Fig. 3D), the electron effective
mass m* for the IFS (m∗
IFS) is determined to be
(0.023 T 0.001)m0 (where m0 is the free electron
mass), following the Lifshitz-Kosevich formula
for a three-dimensional (3D) system (36–38)
AðB,TÞ ¼
Dr
r0
ºðℏwc=EFÞ
1
2
expð−2p2
kBTD=ℏwcÞ
2p2
kBT=ℏwc
sinhð2p2kBT=ℏwcÞ
ð2Þ
Here, r0 is the nonoscillatory component of the
resistivity at B = 0, TD is the Dingle temperature,
kB Boltzmann’s constant, and the cyclotron fre-
quency wc = eB/m*. Considering AIFS = 3.1 ×
10–4
Å–2
, first-principles calculations indicate
EF = 151 meV above the conduction band mini-
mum. At this EF, the calculated m∗
IFS is 0.021m0,
in agreement with the observed value. We can
thus confidently assign this set of SdH oscilla-
tions to the IFS.
In the expression for rxx in 3D systems (36–40)
rxx ¼ r0½1 þ AðB,TÞcos2pðBF=B − d þ gÞŠ
ð3Þ
1/BF is the SdH frequency, and d is a phase shift
determined by the dimensionality, taking the value
d = 0 (or d = T1/8) for the 2D (or 3D) case (41–43).
In this formula, values of |g – d| = |1/2 – fB/2p – d|
EF
A B
kx(Å-1
)ky(Å-1) kx(Å-1
)
kz(Å-1)
Energy(eV)
ky(Å-1
)
Fig. 1. Electronic structure of BiTeI. (A) Energy band dispersion of the conduction band around the
hexagonal face center A point of the BiTeI Brillouin zone. (B) Typical Fermi surface of BiTeI for EF located above
the Dirac point. The Fermi surface consists of an inner Fermi surface (pink pocket) and an outer Fermi surface
(purple-blue pocket). The extremal orbits normal to kz have helical spin textures (arrows), with opposite helicities.
www.sciencemag.org SCIENCE VOL 342 20 DECEMBER 2013 1491
REPORTS
4. between 0 and 1/8 indicate a nontrivial p Berry’s
phase, with the precise value determined by the
degree of two-dimensionality via d. To obtain the
Berry’s phase, the relation between 1/B and
Landau index number n is plotted in Fig. 3E. Here,
peak and valley positions of the oscillation are
determined using –d2
rxx/dB2
(Fig. 3B). We assign
integer indices to the rxx peak positions in 1/B and
half integer indices to the rxx valley positions. The
interpolation line of n versus 1/B in sample A has
an intercept between –1/8 and 0, indicating a non-
trivial Berry’s phase for the IFS. A similar trend is
reproduced for other samples B, C, and D with EF ~
244, 194, and 154 meV, respectively (Fig. 3E). In
a pure Rashba system (g = 0), these results in-
dicate that d deviates from the 3D limit |d| = 1/8,
likely because of the quasi-2D nature of the sys-
tem. In sample B, the SdH oscillation originating
from the IFS can be seen up to 39 T with the re-
spective ∆(1/B) = 0.0259 T–1
, corresponding to a
much larger AIFS = 3.65 × 10–3
Å–2
. The strict
linearity of this index plot up to the quantum limit
is a consequence of negligible Zeeman splitting
and the fact that the OFS dominates the variation of
the chemical potential at this magnetic field. This
allows us to avoid index shifting near the quantum
limit, as observed, for example, in graphite (14), in
much the same manner as has been observed for
specific field orientations of bismuth (11).
Next, we turn to SdH oscillations origi-
nating from the OFS. These oscillations are
clearly observed in the higher–magnetic field
region. Figure 4A shows rxx of sample A up to
56 T at various temperatures. In this case, clear
SdH oscillations are observed above 10 T at 1.5 K
and can be discerned even at 100 K above 40 T. The
oscillatory component is deduced by subtracting a
fourth-order polynomial, as discussed previously,
and is plotted as a function of 1/B in Fig. 4B. The
period of the oscillation [∆(1/B) = 0.00288 T–1
]
correspondstoanOFSextremalcross-sectional area
of AOFS = 3.4 × 10–2
Å–2
, which is very consistent
with the calculated AOFS = 3.43 × 10–2
Å–2
at EF =
151meV.Thisprovidesanimportantself-consistency
check, given that this EF was derived from the IFS
SdH results. From the temperature dependence of
the peak amplitude at 53.6 T, m∗
OFS is determined
to be (0.183 T 0.003)m0 (Fig. 4C), also in good
agreement with the calculated value m* = 0.182m0.
To obtain the Berry’s phase for OFS, the fan dia-
gram is plotted in Fig. 4D. Because a longer
extrapolation is required in the case of the OFS,
we measured five samples with varying EF for
the determination of the intercept value. Here the
integer index n, corresponding to the rxx maximum,
is assigned such that a linear extrapolation of the
index plots yields an intercept closest to zero index
(n = 0). As can be seen in Fig. 4D, the index plots
uniformly exhibit a linear dependence on n with
the lowest integer index n = 6, This linearity again
suggests that the Zeeman effect is negligible and
that the observed oscillations are far from the OFS
Fig.2.SdHoscillations
for the inner and outer
FermisurfacesinBiTeI.
Transverse magnetoresis-
tivity (rxx) of BiTeI with
B || [001] at 1.8 K. Two
types of SdH oscillations
(indicated by arrows)
originate from the inner
and outer Fermi surfaces,
as illustrated in Fig. 1B. 0.66
0.67
0.68
0.69
ρxx
(mΩcm)
B // [001]
IFS
B (T)
OFS
1.8K
0 2 4 6 8 10 12 14
0 20 60
0.00
0.05
0.10
0.15
∆ρxx
/ρxx
(0)(%)
T (K)
B = 3.4 T
0 1 2 6
0.66
0.67
0.68
0.69
23 K
17 K
8 K
ρxx
(mΩcm)
B (T)
1.8 K
B // [001]
A
B DC
E
0
0.0
0.5
1.0
1/B(T
-1
)
D
D
0
C
n
B
A
B
1/ 8
n
A
0
1
2
C
1/B(10
-2
T
-1
)
-1/8
0.0 0 .2 0.4 0 .6
-0.5
0.0
0.5
1.0
∆ρxx
(µΩcm)
1/B (T
-1
)
1.8 K
8 K
15 K
23 K
33 K
45 K
0.0 0 .5 1.0
n=3
n=2.5
n=1.5
n=2
-d
2
ρxx
/dB
2
(a.u.)
1/B (T
-1
)
T = 1.8 K
0
n=1
Sample A
m*=(0.023
+_0.001)m0
-1/8 1/8
0
A: γ-δ = 0.01+_0.03
B: γ-δ = 0.00+_0.05
C: γ-δ = -0.04+_0.05
D: γ-δ = -0.05+_0.03
1 2 3 4 5
3 4 5
40
Fig. 3. Berry’s phase of the inner Fermi surface. (A) rxx of sample A with
B || [001] in the lower–magnetic field region, at various temperatures. The
nonoscillatory background component is deduced at each temperature based
on the SdH node positions (crosses), as shown in the case at 1.8 K. (B)
Negative second derivative of rxx (–d2
rxx/dB2
) as a function of 1/B. a.u.,
arbitrary units. (C) Oscillatory component at various temperatures. (D) Tem-
perature dependence of the SdH oscillation amplitude at 3.4 T [vertical dashed
line in (A)]. (E) Landau index plot of the IFS (error bars are smaller than the
symbol size). Closed circles denote the integer index (rxx peak), and open
circles indicate the half integer index (rxx valley). The intercept is between
–1/8 and 1/8 for samples A and D, as well as for samples with a higher EF
(samples B and C). (Inset) Magnified view around the intercept.
20 DECEMBER 2013 VOL 342 SCIENCE www.sciencemag.org1492
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5. quantum limit. Similar to the case of the IFS, here
again the intercept |g – d| is in the range 0 to 1/8.
Thus, we observe a systematic p-phase shift in SdH
oscillations, consistent with the theoretical predic-
tion that a pure Rashba system will exhibit a non-
trivial p Berry’s phase for both the IFS and OFS.
Observation of this effect is made possible by
the extremely large Rashba energy in BiTeI. It is
interesting to note that, unlike the other candidate
spin Berry’s phase systems such as semiconduc-
tor heterostructures and surface state of topologi-
cal insulators, BiTeI is a 3D electronic system
(albeit, with a quasi-2D electronic structure). Ac-
cordingly, this system may provide the opportunity
to explore the dependence of Berry’s phase on the
trajectory-dependent spin evolution. Moreover,
the prediction that pressure can drive BiTeI through
a quantum phase transition to a topological phase
provides a test to compare Berry’s phase stemming
from different physical origins (35).
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Acknowledgments: We thank J. G. Checkelsky for fruitful
discussions. This work was supported by the Funding Program
for World-Leading Innovative Research and Development on
Science and Technology (FIRST Program), Japan, and the U.S.
Department of Energy, Office of Basic Energy Sciences,
Materials Sciences and Engineering Division, under contract
DE-AC02-76SF00515 (C.B. and H.Y.H). This research was
partly supported by Grants-in-Aid for Scientific Research (B)
(no. 23340096) and (S) (no. 24224009) from the Ministry of
Education, Culture, Sports, Science and Technology, Japan.
Supplementary Materials
www.sciencemag.org/content/342/6165/1490/suppl/DC1
Materials and Methods
Figs. S1 to S3
Reference (44)
31 July 2012; accepted 18 November 2013
10.1126/science.1242247
A
B
D
C
106 8420 12 14
0.00
0.02
0.04
0.06
0 1/8-1/8
-1/8
0
1/8
F
F
E
C
B
A
E
C
B
A
1/B(mT
-1
)
1/B(T
-1
)
n
n
0
1
0 10
0.8
1.0
1.2
B // [001]
ρ
xx
(mΩcm)
B (T)
30 K
100K
80 K
50 K
1.5 Sample AK
0.02 0.03 0.04
-50
0
50
∆ρ
xx
(µΩcm)
1/B (T
-1
)
80K
100K
1.5K
30 K
50 K
0 50 100 150
0
2
4
6
8
∆ρxx
/ρxx
(0)(%)
B = 53.6 T
m*=(0.183
+_0.003)m0
T (K)
20 30 40 50 60
A: γ-δ = 0.01+_0.03
B: γ-δ = -0.02+_0.06
C: γ-δ = -0.09+_0.04
E: γ-δ = 0.01+_0.04
F: γ-δ = -0.03+_0.04
Fig. 4. Berry’s phase of the outer Fermi surface. (A) rxx of sample A
with B || [001] up to 56 T at various temperatures. (B) The oscillatory
component as a function of 1/B. (C) Temperature dependence of the oscillation
amplitude at 53.6 T. (D) Landau index plots of the OFS with various EF
samples A, B, C, E, and F. Closed circles denote the integer index (rxx
peak), and open circles indicate the half integer index (rxx valley). The
integer index n is assigned such that a linear extrapolation of the index
plots yields an intercept closest to zero index (n = 0). (Inset) Magnified
view around the intercept, showing an intercept between –1/8 and 1/8 for
all samples.
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