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  1. Article ; Online: What's the best chatbot for me? Researchers put LLMs through their paces.

    Humphries, Elizabeth M / Wright, Carrie / Hoffman, Ava M / Savonen, Candace / Leek, Jeffrey T

    Nature

    2023  

    Language English
    Publishing date 2023-09-27
    Publishing country England
    Document type News
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-023-03023-4
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  2. Book ; Online: Motivation, inclusivity, and realism should drive data science education

    Savonen, Candace / Wright, Carrie / Hoffman, Ava M. / Humphries, Elizabeth M. / Cox, Katherine E. L. / Tan, Frederick J. / Leek, Jeffrey T.

    2023  

    Abstract: Data science education provides tremendous opportunities but remains inaccessible to many communities. Increasing the accessibility of data science to these communities not only benefits the individuals entering data science, but also increases the field' ...

    Abstract Data science education provides tremendous opportunities but remains inaccessible to many communities. Increasing the accessibility of data science to these communities not only benefits the individuals entering data science, but also increases the field's innovation and potential impact as a whole. Education is the most scalable solution to meet these needs, but many data science educators lack formal training in education. Our group has led education efforts for a variety of audiences: from professional scientists to high school students to lay audiences. These experiences have helped form our teaching philosophy which we have summarized into three main ideals: 1) motivation, 2) inclusivity, and 3) realism. To put these ideals better into practice, we also aim to iteratively update our teaching approaches and curriculum as we find ways to better reach these ideals. In this manuscript we discuss these ideals as well practical ideas for how to implement these philosophies in the classroom.

    Comment: This has been submitted to F1000 and is under review (as of 5/9/23)
    Keywords Computer Science - Computers and Society ; Physics - Physics Education
    Subject code 306
    Publishing date 2023-05-09
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Predicting Heterogeneity in Patient Response to Morphine Treatment for Neonatal Opioid Withdrawal Syndrome.

    Smolyak, Daniel / Humphries, Elizabeth M / Parikh, Abhinav / Gopalakrishnan, Mathangi / Aycan, Fulden / Bjarnadóttir, Margrét / Ament, Seth A / El-Metwally, Dina / Beitelshees, Amber / Agarwal, Ritu

    Clinical pharmacology and therapeutics

    2023  Volume 114, Issue 5, Page(s) 1015–1022

    Abstract: Infants with neonatal opioid withdrawal syndrome commonly receive morphine treatment to manage their withdrawal signs. However, the effectiveness of this pharmacotherapy in managing the infants' withdrawal signs vary widely. We sought to understand how ... ...

    Abstract Infants with neonatal opioid withdrawal syndrome commonly receive morphine treatment to manage their withdrawal signs. However, the effectiveness of this pharmacotherapy in managing the infants' withdrawal signs vary widely. We sought to understand how information available early in infant monitoring can anticipate this treatment response, focusing on early modified Finnegan Neonatal Abstinence Scoring System (FNASS) scores, polygenic risk for opioid dependence (polygenic risk score (PRS)), and drug exposure. Using k-means clustering, we divided the 213 infants in our cohort into 3 groups based on their FNASS scores in the 12 hours before and after the initiation of pharmacotherapy. We found that these groups were pairwise significantly different for risk factors, including methadone exposure, and for in-hospital outcomes, including total morphine received, length of stay, and highest FNASS score. Whereas PRS was not predictive of receipt of treatment, PRS was pairwise significantly different between a subset of the groups. Using tree-based machine learning methods, we then constructed network graphs of the relationships among these groups, FNASS scores, PRS, drug exposures, and in-hospital outcomes. The resulting networks also showed meaningful connection between early FNASS scores and PRS, as well as between both of those and later in-hospital outcomes. These analyses present clinicians with the opportunity to better anticipate infant withdrawal progression and prepare accordingly, whether with expedited morphine treatment or non-pharmacotherapeutic alternative treatments.
    Language English
    Publishing date 2023-07-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 123793-7
    ISSN 1532-6535 ; 0009-9236
    ISSN (online) 1532-6535
    ISSN 0009-9236
    DOI 10.1002/cpt.3007
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  4. Article ; Online ; Research data: (with research data) Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds.

    Humphries, Elizabeth M / Winker, Kevin

    Molecular ecology

    2011  Volume 20, Issue 3, Page(s) 573–583

    Abstract: Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically ... ...

    Abstract Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.
    MeSH term(s) Amplified Fragment Length Polymorphism Analysis ; Animals ; Anseriformes/classification ; Anseriformes/genetics ; Birds/classification ; Birds/genetics ; Cell Nucleus/genetics ; Charadriiformes/classification ; Charadriiformes/genetics ; DNA/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Genome ; Mitochondria, Muscle/genetics ; Passeriformes/classification ; Passeriformes/genetics ; Phenotype ; Sequence Analysis, DNA
    Chemical Substances DNA, Mitochondrial ; DNA (9007-49-2)
    Language English
    Publishing date 2011-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083 ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/j.1365-294X.2010.04965.x
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  5. Article ; Research data: (with research data) Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds

    Humphries, Elizabeth M / Winker, Kevin

    Molecular ecology. 2011 Feb., v. 20, no. 3

    2011  

    Abstract: Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically ... ...

    Abstract Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.
    Keywords Anseriformes ; Charadriiformes ; Passeriformes ; amplified fragment length polymorphism ; birds ; genetic variation ; indicator species ; nucleotide sequences ; phenotype ; sorting
    Language English
    Dates of publication 2011-02
    Size p. 573-583.
    Publishing place Blackwell Publishing Ltd
    Document type Article ; Research data
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083 ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/j.1365-294X.2010.04965.x
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  6. Article ; Online: Working through polytomies: auklets revisited.

    Humphries, Elizabeth M / Winker, Kevin

    Molecular phylogenetics and evolution

    2010  Volume 54, Issue 1, Page(s) 88–96

    Abstract: Polytomies, or phylogenetic "bushes", are the result of a series of internodes occurring in a short period of evolutionary time (which can result in data that do not contain enough information), or data that have too much homoplasy to resolve a ... ...

    Abstract Polytomies, or phylogenetic "bushes", are the result of a series of internodes occurring in a short period of evolutionary time (which can result in data that do not contain enough information), or data that have too much homoplasy to resolve a bifurcating branching pattern. In this study we used the Aethia auklet polytomy to explore the effectiveness of different methods for resolving polytomies: mitochondrial DNA gene choice, number of individuals per species sampled, model of molecular evolution, and AFLP loci. We recovered a fully-resolved phylogeny using NADH dehydrogenase subunit 2 (ND2) sequence data under two different Bayesian models. We were able to corroborate this tree under one model with an expanded mtDNA dataset. Effectiveness of additional intraspecific sampling varied with node, and fully 20% of the subsampled datasets failed to return a congruent phylogeny when we sampled only one or two individuals per species. We did not recover a resolved phylogeny using AFLP data. Conflict in the AFLP dataset showed that nearly all possible relationships were supported at low levels of confidence, suggesting that either AFLPs are not useful at the genetic depth of the Aethia auklet radiation (7-9% divergent in the mtDNA ND2 gene), perhaps resulting in too much homoplasy, or that the Aethia auklets have experienced incomplete lineage sorting at many nuclear loci.
    MeSH term(s) Amplified Fragment Length Polymorphism Analysis ; Animals ; Bayes Theorem ; Charadriiformes/classification ; Charadriiformes/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Models, Genetic ; NADH Dehydrogenase/genetics ; Phylogeny ; Sequence Analysis, DNA
    Chemical Substances DNA, Mitochondrial ; NADH Dehydrogenase (EC 1.6.99.3)
    Language English
    Publishing date 2010-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 33610-5
    ISSN 1095-9513 ; 1055-7903
    ISSN (online) 1095-9513
    ISSN 1055-7903
    DOI 10.1016/j.ympev.2009.07.023
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    Zs.A 3644: Show issues Location:
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  7. Article ; Online: Genome-wide significant risk loci for mood disorders in the Old Order Amish founder population.

    Humphries, Elizabeth M / Ahn, Kwangmi / Kember, Rachel L / Lopes, Fabiana L / Mocci, Evelina / Peralta, Juan M / Blangero, John / Glahn, David C / Goes, Fernando S / Zandi, Peter P / Kochunov, Peter / Van Hout, Cristopher / Shuldiner, Alan R / Pollin, Toni I / Mitchell, Braxton D / Bucan, Maja / Hong, L Elliot / McMahon, Francis J / Ament, Seth A

    Molecular psychiatry

    2023  Volume 28, Issue 12, Page(s) 5262–5271

    Abstract: Genome-wide association studies (GWAS) of mood disorders in large case-control cohorts have identified numerous risk loci, yet pathophysiological mechanisms remain elusive, primarily due to the very small effects of common variants. We sought to discover ...

    Abstract Genome-wide association studies (GWAS) of mood disorders in large case-control cohorts have identified numerous risk loci, yet pathophysiological mechanisms remain elusive, primarily due to the very small effects of common variants. We sought to discover risk variants with larger effects by conducting a genome-wide association study of mood disorders in a founder population, the Old Order Amish (OOA, n = 1,672). Our analysis revealed four genome-wide significant risk loci, all of which were associated with >2-fold relative risk. Quantitative behavioral and neurocognitive assessments (n = 314) revealed effects of risk variants on sub-clinical depressive symptoms and information processing speed. Network analysis suggested that OOA-specific risk loci harbor novel risk-associated genes that interact with known neuropsychiatry-associated genes via gene interaction networks. Annotation of the variants at these risk loci revealed population-enriched, non-synonymous variants in two genes encoding neurodevelopmental transcription factors, CUX1 and CNOT1. Our findings provide insight into the genetic architecture of mood disorders and a substrate for mechanistic and clinical studies.
    MeSH term(s) Humans ; Genome-Wide Association Study/methods ; Male ; Female ; Genetic Predisposition to Disease/genetics ; Mood Disorders/genetics ; Middle Aged ; Polymorphism, Single Nucleotide/genetics ; Amish/genetics ; Adult ; Case-Control Studies ; Transcription Factors/genetics ; Risk Factors ; Genetic Loci ; Repressor Proteins/genetics ; Aged ; Homeodomain Proteins/genetics ; Founder Effect ; Nuclear Proteins/genetics
    Chemical Substances Transcription Factors ; Repressor Proteins ; Homeodomain Proteins ; Nuclear Proteins
    Language English
    Publishing date 2023-03-07
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1330655-8
    ISSN 1476-5578 ; 1359-4184
    ISSN (online) 1476-5578
    ISSN 1359-4184
    DOI 10.1038/s41380-023-02014-1
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  8. Article ; Online: Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder.

    Hasin, Naushaba / Riggs, Lace M / Shekhtman, Tatyana / Ashworth, Justin / Lease, Robert / Oshone, Rediet T / Humphries, Elizabeth M / Badner, Judith A / Thomson, Pippa A / Glahn, David C / Craig, David W / Edenberg, Howard J / Gershon, Elliot S / McMahon, Francis J / Nurnberger, John I / Zandi, Peter P / Kelsoe, John R / Roach, Jared C / Gould, Todd D /
    Ament, Seth A

    Molecular psychiatry

    2022  Volume 27, Issue 9, Page(s) 3842–3856

    Abstract: Bipolar disorder is an often-severe mental health condition characterized by alternation between extreme mood states of mania and depression. Despite strong heritability and the recent identification of 64 common variant risk loci of small effect, ... ...

    Abstract Bipolar disorder is an often-severe mental health condition characterized by alternation between extreme mood states of mania and depression. Despite strong heritability and the recent identification of 64 common variant risk loci of small effect, pathophysiological mechanisms remain unknown. Here, we analyzed genome sequences from 41 multiply-affected pedigrees and identified variants in 741 genes with nominally significant linkage or association with bipolar disorder. These 741 genes overlapped known risk genes for neurodevelopmental disorders and clustered within gene networks enriched for synaptic and nuclear functions. The top variant in this analysis - prioritized by statistical association, predicted deleteriousness, and network centrality - was a missense variant in the gene encoding D-amino acid oxidase (DAO
    MeSH term(s) Mice ; Animals ; Humans ; Receptors, N-Methyl-D-Aspartate/genetics ; Receptors, N-Methyl-D-Aspartate/metabolism ; Bipolar Disorder/genetics ; Bipolar Disorder/metabolism ; D-Amino-Acid Oxidase/genetics ; D-Amino-Acid Oxidase/metabolism ; Gene Regulatory Networks/genetics ; Cerebellum/metabolism
    Chemical Substances Receptors, N-Methyl-D-Aspartate ; D-Amino-Acid Oxidase (EC 1.4.3.3)
    Language English
    Publishing date 2022-05-11
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
    ZDB-ID 1330655-8
    ISSN 1476-5578 ; 1359-4184
    ISSN (online) 1476-5578
    ISSN 1359-4184
    DOI 10.1038/s41380-022-01609-4
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  9. Article: Multilocus phylogeography of a holarctic duck: colonization of north america from eurasia by gadwall (Anas strepera).

    Peters, Jeffrey L / Zhuravlev, Yuri N / Fefelov, Igor / Humphries, Elizabeth M / Omland, Kevin E

    Evolution; international journal of organic evolution

    2008  Volume 62, Issue 6, Page(s) 1469–1483

    Abstract: More than 100 species of birds have Holarctic distributions extending across Eurasia and North America, and many of them likely achieved these distributions by recently colonizing one continent from the other. Mitochondrial DNA (mtDNA) and five nuclear ... ...

    Abstract More than 100 species of birds have Holarctic distributions extending across Eurasia and North America, and many of them likely achieved these distributions by recently colonizing one continent from the other. Mitochondrial DNA (mtDNA) and five nuclear introns were sequenced to test the direction and timing of colonization for a Holarctic duck, the gadwall (Anas strepera). Three lines of evidence suggest gadwalls colonized North America from Eurasia. First, New World (NW) gadwalls had fewer alleles at every locus and 61% of the allelic richness found in Old World (OW) gadwalls. Second, NW gadwalls had lower mtDNA allelic richness than other NW ducks. Third, coalescent analysis suggested that less than 5% of the ancestral population contributed to NW gadwalls at the time of divergence. Gadwalls likely colonized North America during the Late Pleistocene (approximately 81,000 years ago), but the confidence interval on that estimate was large (8500-450,000 years ago). Intercontinental gene flow and selection also likely contributed to genetic diversity in gadwalls. This study illustrates the use of multiple loci and coalescent analyses for critically testing a priori hypotheses regarding dispersal and colonization and provides an independent datapoint supporting an OW to NW bias in the direction of colonization.
    MeSH term(s) Animals ; Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Demography ; Ducks/genetics ; Europe ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Models, Genetic ; Molecular Sequence Data ; North America ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity
    Chemical Substances DNA Primers ; DNA, Mitochondrial
    Language English
    Publishing date 2008-06
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2036375-8
    ISSN 1558-5646 ; 0014-3820
    ISSN (online) 1558-5646
    ISSN 0014-3820
    DOI 10.1111/j.1558-5646.2008.00372.x
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