Update README.md

README.md

@@ -11,277 +11,327 @@ base_model: thenlper/gte-base
 widget:
 - source_sentence: Molecular phylogenetic resolution of the mega-diverse clade Apoditrysia
   sentences:
-  - In a previous study of higher-level arthropod phylogeny, analyses of nucleotide
-    sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded
-    significantly higher bootstrap support for selected nodes than did amino acids.
-    This study investigates the cause of that discrepancy. The hypothesis is tested
-    that failure to distinguish the serine residues encoded by two disjunct clusters
-    of codons (TCN, AGY) in amino acid analyses leads to this discrepancy. In one
-    test, the two clusters of serine codons (Ser1, Ser2) are conceptually translated
-    as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows
-    striking increases in bootstrap support, in some cases matching that in nucleotide
-    analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially
-    altered through targeted deletions, modifications, and replacements, revealing
-    the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous
-    methods of coding nonsynonymous nucleotide change are robust and computationally
-    efficient by introducing two new degeneracy coding methods. We demonstrate for
-    degeneracy coding that neither compositional heterogeneity at the level of nucleotides
-    nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately
-    coded amino acids) is a major source of non-phylogenetic signal. The incongruity
-    in support between amino-acid and nucleotide analyses of the forementioned arthropod
-    data set is resolved by showing that "standard" 20-amino-acid analyses yield lower
-    node support specifically when serine provides crucial signal. Separate coding
-    of Ser1 and Ser2 residues yields support commensurate with that found by degenerated
-    nucleotides, without introducing phylogenetic artifacts. While exclusion of all
-    serine data leads to reduced support for serine-sensitive nodes, these nodes are
-    still recovered in the ML topology, indicating that the enhanced signal from Ser1
-    and Ser2 is not qualitatively different from that of the other amino acids.
-  - 'Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly
-    resolved family-level divergences within most superfamilies, and most divergences
-    among the relatively species-poor early-arising superfamilies. In sharp contrast,
-    relationships among the superfamilies of more advanced moths and butterflies that
-    comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly
-    supported. This uncertainty, in turn, limits our ability to discern the origins,
-    ages and evolutionary consequences of traits hypothesized to promote the spectacular
-    diversification of Apoditrysia. Low support along the apoditrysian "backbone"
-    probably reflects rapid diversification. If so, it may be feasible to strengthen
-    resolution by radically increasing the gene sample, but case studies have been
-    few. We explored the potential of next-generation sequencing to conclusively resolve
-    apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively
-    orthologous gene sequences across a broad sample of 40 apoditrysians plus four
-    outgroups, to which we added two taxa from previously published data. Phylogenetic
-    analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated
-    ortholog groups containing any apparent paralogs, yielded dramatic overall increase
-    in bootstrap support for deeper nodes within Apoditrysia as compared to results
-    from previous and concurrent 19-gene analyses. High support was restricted mainly
-    to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending
-    multiple superfamilies had bootstrap support of 100%. The strongly supported nodes
-    showed little conflict with groupings from previous studies, and were little affected
-    by changes in taxon sampling, suggesting that they reflect true signal rather
-    than artifacts of massive gene sampling. In contrast, strong support was seen
-    at only 2 of 11 deeper nodes among the "lower", non-obtectomeran apoditrysians.
-    These represent a much harder phylogenetic problem, for which one path to resolution
-    might include further increase in gene sampling, together with improved orthology
-    assignments. '
-  - 'One of the major challenges in cell implantation therapies is to promote integration
-    of the microcirculation between the implanted cells and the host. We used adipose-derived
-    stromal vascular fraction (SVF) cells to vascularize a human liver cell (HepG2)
-    implant. We hypothesized that the SVF cells would form a functional microcirculation
-    via vascular assembly and inosculation with the host vasculature. Initially, we
-    assessed the extent and character of neovasculatures formed by freshly isolated
-    and cultured SVF cells and found that freshly isolated cells have a higher vascularization
-    potential. Generation of a 3D implant containing fresh SVF and HepG2 cells formed
-    a tissue in which HepG2 cells were entwined with a network of microvessels. Implanted
-    HepG2 cells sequestered labeled LDL delivered by systemic intravascular injection
-    only in SVF-vascularized implants demonstrating that SVF cell-derived vasculatures
-    can effectively integrate with host vessels and interface with parenchymal cells
-    to form a functional tissue mimic. '
+  - >-
+    In a previous study of higher-level arthropod phylogeny, analyses of
+    nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod
+    species yielded significantly higher bootstrap support for selected nodes
+    than did amino acids. This study investigates the cause of that discrepancy.
+    The hypothesis is tested that failure to distinguish the serine residues
+    encoded by two disjunct clusters of codons (TCN, AGY) in amino acid analyses
+    leads to this discrepancy. In one test, the two clusters of serine codons
+    (Ser1, Ser2) are conceptually translated as separate amino acids. Analysis
+    of the resulting 21-amino-acid data matrix shows striking increases in
+    bootstrap support, in some cases matching that in nucleotide analyses. In a
+    second approach, nucleotide and 20-amino-acid data sets are artificially
+    altered through targeted deletions, modifications, and replacements,
+    revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We
+    confirm that previous methods of coding nonsynonymous nucleotide change are
+    robust and computationally efficient by introducing two new degeneracy
+    coding methods. We demonstrate for degeneracy coding that neither
+    compositional heterogeneity at the level of nucleotides nor codon usage bias
+    between Ser1 and Ser2 clusters of codons (or their separately coded amino
+    acids) is a major source of non-phylogenetic signal. The incongruity in
+    support between amino-acid and nucleotide analyses of the forementioned
+    arthropod data set is resolved by showing that "standard" 20-amino-acid
+    analyses yield lower node support specifically when serine provides crucial
+    signal. Separate coding of Ser1 and Ser2 residues yields support
+    commensurate with that found by degenerated nucleotides, without introducing
+    phylogenetic artifacts. While exclusion of all serine data leads to reduced
+    support for serine-sensitive nodes, these nodes are still recovered in the
+    ML topology, indicating that the enhanced signal from Ser1 and Ser2 is not
+    qualitatively different from that of the other amino acids.
+  - >-
+    Recent molecular phylogenetic studies of the insect order Lepidoptera have
+    robustly resolved family-level divergences within most superfamilies, and
+    most divergences among the relatively species-poor early-arising
+    superfamilies. In sharp contrast, relationships among the superfamilies of
+    more advanced moths and butterflies that comprise the mega-diverse clade
+    Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This
+    uncertainty, in turn, limits our ability to discern the origins, ages and
+    evolutionary consequences of traits hypothesized to promote the spectacular
+    diversification of Apoditrysia. Low support along the apoditrysian
+    "backbone" probably reflects rapid diversification. If so, it may be
+    feasible to strengthen resolution by radically increasing the gene sample,
+    but case studies have been few. We explored the potential of next-generation
+    sequencing to conclusively resolve apoditrysian relationships. We used
+    transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences
+    across a broad sample of 40 apoditrysians plus four outgroups, to which we
+    added two taxa from previously published data. Phylogenetic analysis of a
+    46-taxon, 741-gene matrix, resulting from a strict filter that eliminated
+    ortholog groups containing any apparent paralogs, yielded dramatic overall
+    increase in bootstrap support for deeper nodes within Apoditrysia as
+    compared to results from previous and concurrent 19-gene analyses. High
+    support was restricted mainly to the huge subclade Obtectomera broadly
+    defined, in which 11 of 12 nodes subtending multiple superfamilies had
+    bootstrap support of 100%. The strongly supported nodes showed little
+    conflict with groupings from previous studies, and were little affected by
+    changes in taxon sampling, suggesting that they reflect true signal rather
+    than artifacts of massive gene sampling. In contrast, strong support was
+    seen at only 2 of 11 deeper nodes among the "lower", non-obtectomeran
+    apoditrysians. These represent a much harder phylogenetic problem, for which
+    one path to resolution might include further increase in gene sampling,
+    together with improved orthology assignments. 
+  - >-
+    One of the major challenges in cell implantation therapies is to promote
+    integration of the microcirculation between the implanted cells and the
+    host. We used adipose-derived stromal vascular fraction (SVF) cells to
+    vascularize a human liver cell (HepG2) implant. We hypothesized that the SVF
+    cells would form a functional microcirculation via vascular assembly and
+    inosculation with the host vasculature. Initially, we assessed the extent
+    and character of neovasculatures formed by freshly isolated and cultured SVF
+    cells and found that freshly isolated cells have a higher vascularization
+    potential. Generation of a 3D implant containing fresh SVF and HepG2 cells
+    formed a tissue in which HepG2 cells were entwined with a network of
+    microvessels. Implanted HepG2 cells sequestered labeled LDL delivered by
+    systemic intravascular injection only in SVF-vascularized implants
+    demonstrating that SVF cell-derived vasculatures can effectively integrate
+    with host vessels and interface with parenchymal cells to form a functional
+    tissue mimic. 
 - source_sentence: Exosomes as drug delivery systems for gastrointestinal cancers
   sentences:
-  - Gastrointestinal cancer is one of the most common malignancies with relatively
-    high morbidity and mortality. Exosomes are nanosized extracellular vesicles derived
-    from most cells and widely distributed in body fluids. They are natural endogenous
-    nanocarriers with low immunogenicity, high biocompatibility, and natural targeting,
-    and can transport lipids, proteins, DNA, and RNA. Exosomes contain DNA, RNA, proteins,
-    lipids, and other bioactive components, which can play a role in information transmission
-    and regulation of cellular physiological and pathological processes during the
-    progression of gastrointestinal cancer. In this paper, the role of exosomes in
-    gastrointestinal cancers is briefly reviewed, with emphasis on the application
-    of exosomes as drug delivery systems for gastrointestinal cancers. Finally, the
-    challenges faced by exosome-based drug delivery systems are discussed.
-  - Background In the myocardium, pericytes are often confused with other interstitial
-    cell types, such as fibroblasts. The lack of well-characterized and specific tools
-    for identification, lineage tracing, and conditional targeting of myocardial pericytes
-    has hampered studies on their role in heart disease. In the current study, we
-    characterize and validate specific and reliable strategies for labeling and targeting
-    of cardiac pericytes. Methods and Results Using the neuron-glial antigen 2 (NG2)
-  - Exosomes are small extracellular vesicles with diameters of 30-150 nm. In both
-    physiological and pathological conditions, nearly all types of cells can release
-    exosomes, which play important roles in cell communication and epigenetic regulation
-    by transporting crucial protein and genetic materials such as miRNA, mRNA, and
-    DNA. Consequently, exosome-based disease diagnosis and therapeutic methods have
-    been intensively investigated. However, as in any natural science field, the in-depth
-    investigation of exosomes relies heavily on technological advances. Historically,
-    the two main technical hindrances that have restricted the basic and applied researches
-    of exosomes include, first, how to simplify the extraction and improve the yield
-    of exosomes and, second, how to effectively distinguish exosomes from other extracellular
-    vesicles, especially functional microvesicles. Over the past few decades, although
-    a standardized exosome isolation method has still not become available, a number
-    of techniques have been established through exploration of the biochemical and
-    physicochemical features of exosomes. In this work, by comprehensively analyzing
-    the progresses in exosome separation strategies, we provide a panoramic view of
-    current exosome isolation techniques, providing perspectives toward the development
-    of novel approaches for high-efficient exosome isolation from various types of
-    biological matrices. In addition, from the perspective of exosome-based diagnosis
-    and therapeutics, we emphasize the issue of quantitative exosome and microvesicle
-    separation.
-- source_sentence: Comparison of pesticide active substances in conventional agriculture
-    and organic agriculture in Europe
+  - >-
+    Gastrointestinal cancer is one of the most common malignancies with
+    relatively high morbidity and mortality. Exosomes are nanosized
+    extracellular vesicles derived from most cells and widely distributed in
+    body fluids. They are natural endogenous nanocarriers with low
+    immunogenicity, high biocompatibility, and natural targeting, and can
+    transport lipids, proteins, DNA, and RNA. Exosomes contain DNA, RNA,
+    proteins, lipids, and other bioactive components, which can play a role in
+    information transmission and regulation of cellular physiological and
+    pathological processes during the progression of gastrointestinal cancer. In
+    this paper, the role of exosomes in gastrointestinal cancers is briefly
+    reviewed, with emphasis on the application of exosomes as drug delivery
+    systems for gastrointestinal cancers. Finally, the challenges faced by
+    exosome-based drug delivery systems are discussed.
+  - >-
+    Background In the myocardium, pericytes are often confused with other
+    interstitial cell types, such as fibroblasts. The lack of well-characterized
+    and specific tools for identification, lineage tracing, and conditional
+    targeting of myocardial pericytes has hampered studies on their role in
+    heart disease. In the current study, we characterize and validate specific
+    and reliable strategies for labeling and targeting of cardiac pericytes.
+    Methods and Results Using the neuron-glial antigen 2 (NG2)
+  - >-
+    Exosomes are small extracellular vesicles with diameters of 30-150 nm. In
+    both physiological and pathological conditions, nearly all types of cells
+    can release exosomes, which play important roles in cell communication and
+    epigenetic regulation by transporting crucial protein and genetic materials
+    such as miRNA, mRNA, and DNA. Consequently, exosome-based disease diagnosis
+    and therapeutic methods have been intensively investigated. However, as in
+    any natural science field, the in-depth investigation of exosomes relies
+    heavily on technological advances. Historically, the two main technical
+    hindrances that have restricted the basic and applied researches of exosomes
+    include, first, how to simplify the extraction and improve the yield of
+    exosomes and, second, how to effectively distinguish exosomes from other
+    extracellular vesicles, especially functional microvesicles. Over the past
+    few decades, although a standardized exosome isolation method has still not
+    become available, a number of techniques have been established through
+    exploration of the biochemical and physicochemical features of exosomes. In
+    this work, by comprehensively analyzing the progresses in exosome separation
+    strategies, we provide a panoramic view of current exosome isolation
+    techniques, providing perspectives toward the development of novel
+    approaches for high-efficient exosome isolation from various types of
+    biological matrices. In addition, from the perspective of exosome-based
+    diagnosis and therapeutics, we emphasize the issue of quantitative exosome
+    and microvesicle separation.
+- source_sentence: >-
+    Comparison of pesticide active substances in conventional agriculture and
+    organic agriculture in Europe
   sentences:
-  - Total concentrations of metals in soil are poor predictors of toxicity. In the
-    last decade, considerable effort has been made to demonstrate how metal toxicity
-    is affected by the abiotic properties of soil. Here this information is collated
-    and shows how these data have been used in the European Union for defining predicted-no-effect
-    concentrations (PNECs) of Cd, Cu, Co, Ni, Pb, and Zn in soil. Bioavailability
-    models have been calibrated using data from more than 500 new chronic toxicity
-    tests in soils amended with soluble metal salts, in experimentally aged soils,
-    and in field-contaminated soils. In general, soil pH was a good predictor of metal
-    solubility but a poor predictor of metal toxicity across soils. Toxicity thresholds
-    based on the free metal ion activity were generally more variable than those expressed
-    on total soil metal, which can be explained, but not predicted, using the concept
-    of the biotic ligand model. The toxicity thresholds based on total soil metal
-    concentrations rise almost proportionally to the effective cation exchange capacity
-    of soil. Total soil metal concentrations yielding 10% inhibition in freshly amended
-    soils were up to 100-fold smaller (median 3.4-fold, n = 110 comparative tests)
-    than those in corresponding aged soils or field-contaminated soils. The change
-    in isotopically exchangeable metal in soil proved to be a conservative estimate
-    of the change in toxicity upon aging. The PNEC values for specific soil types
-    were calculated using this information. The corrections for aging and for modifying
-    effects of soil properties in metal-salt-amended soils are shown to be the main
-    factors by which PNEC values rise above the natural background range.
-  - There is much debate about whether the (mostly synthetic) pesticide active substances
-    (AS) in conventional agriculture have different non-target effects than the natural
-    AS in organic agriculture. We evaluated the official EU pesticide database to
-    compare 256 AS that may only be used on conventional farmland with 134 AS that
-    are permitted on organic farmland. As a benchmark, we used (i) the hazard classifications
-    of the Globally Harmonized System (GHS), and (ii) the dietary and occupational
-    health-based guidance values, which were established in the authorization procedure.
-    Our comparison showed that 55% of the AS used only in conventional agriculture
-    contained health or environmental hazard statements, but only 3% did of the AS
-    authorized for organic agriculture. Warnings about possible harm to the unborn
-    child, suspected carcinogenicity, or acute lethal effects were found in 16% of
-    the AS used in conventional agriculture, but none were found in organic agriculture.
-    Furthermore, the establishment of health-based guidance values for dietary and
-    non-dietary exposures were relevant by the European authorities for 93% of conventional
-    AS, but only for 7% of organic AS. We, therefore, encourage policies and strategies
-    to reduce the use and risk of pesticides, and to strengthen organic farming in
-    order to protect biodiversity and maintain food security.
-  - Herpes simplex virus 1 (HSV-1) encodes Us3 protein kinase, which is critical for
-    viral pathogenicity in both mouse peripheral sites (e.g., eyes and vaginas) and
-    in the central nervous systems (CNS) of mice after intracranial and peripheral
-    inoculations, respectively. Whereas some Us3 substrates involved in Us3 pathogenicity
-    in peripheral sites have been reported, those involved in Us3 pathogenicity in
-    the CNS remain to be identified. We recently reported that Us3 phosphorylated
-    HSV-1 dUTPase (vdUTPase) at serine 187 (Ser-187) in infected cells, and this phosphorylation
-    promoted viral replication by regulating optimal enzymatic activity of vdUTPase.
-    In the present study, we show that the replacement of vdUTPase Ser-187 by alanine
-    (S187A) significantly reduced viral replication and virulence in the CNS of mice
-    following intracranial inoculation and that the phosphomimetic substitution at
-    vdUTPase Ser-187 in part restored the wild-type viral replication and virulence.
-    Interestingly, the S187A mutation in vdUTPase had no effect on viral replication
-    and pathogenic effects in the eyes and vaginas of mice after ocular and vaginal
-    inoculation, respectively. Similarly, the enzyme-dead mutation in vdUTPase significantly
-    reduced viral replication and virulence in the CNS of mice after intracranial
-    inoculation, whereas the mutation had no effect on viral replication and pathogenic
-    effects in the eyes and vaginas of mice after ocular and vaginal inoculation,
-    respectively. These observations suggested that vdUTPase was one of the Us3 substrates
-    responsible for Us3 pathogenicity in the CNS and that the CNS-specific virulence
-    of HSV-1 involved strict regulation of vdUTPase activity by Us3 phosphorylation.
-- source_sentence: Load-dependent detachment and reattachment kinetics of kinesin-1,
-    -2 and 3 motors
+  - >-
+    Total concentrations of metals in soil are poor predictors of toxicity. In
+    the last decade, considerable effort has been made to demonstrate how metal
+    toxicity is affected by the abiotic properties of soil. Here this
+    information is collated and shows how these data have been used in the
+    European Union for defining predicted-no-effect concentrations (PNECs) of
+    Cd, Cu, Co, Ni, Pb, and Zn in soil. Bioavailability models have been
+    calibrated using data from more than 500 new chronic toxicity tests in soils
+    amended with soluble metal salts, in experimentally aged soils, and in
+    field-contaminated soils. In general, soil pH was a good predictor of metal
+    solubility but a poor predictor of metal toxicity across soils. Toxicity
+    thresholds based on the free metal ion activity were generally more variable
+    than those expressed on total soil metal, which can be explained, but not
+    predicted, using the concept of the biotic ligand model. The toxicity
+    thresholds based on total soil metal concentrations rise almost
+    proportionally to the effective cation exchange capacity of soil. Total soil
+    metal concentrations yielding 10% inhibition in freshly amended soils were
+    up to 100-fold smaller (median 3.4-fold, n = 110 comparative tests) than
+    those in corresponding aged soils or field-contaminated soils. The change in
+    isotopically exchangeable metal in soil proved to be a conservative estimate
+    of the change in toxicity upon aging. The PNEC values for specific soil
+    types were calculated using this information. The corrections for aging and
+    for modifying effects of soil properties in metal-salt-amended soils are
+    shown to be the main factors by which PNEC values rise above the natural
+    background range.
+  - >-
+    There is much debate about whether the (mostly synthetic) pesticide active
+    substances (AS) in conventional agriculture have different non-target
+    effects than the natural AS in organic agriculture. We evaluated the
+    official EU pesticide database to compare 256 AS that may only be used on
+    conventional farmland with 134 AS that are permitted on organic farmland. As
+    a benchmark, we used (i) the hazard classifications of the Globally
+    Harmonized System (GHS), and (ii) the dietary and occupational health-based
+    guidance values, which were established in the authorization procedure. Our
+    comparison showed that 55% of the AS used only in conventional agriculture
+    contained health or environmental hazard statements, but only 3% did of the
+    AS authorized for organic agriculture. Warnings about possible harm to the
+    unborn child, suspected carcinogenicity, or acute lethal effects were found
+    in 16% of the AS used in conventional agriculture, but none were found in
+    organic agriculture. Furthermore, the establishment of health-based guidance
+    values for dietary and non-dietary exposures were relevant by the European
+    authorities for 93% of conventional AS, but only for 7% of organic AS. We,
+    therefore, encourage policies and strategies to reduce the use and risk of
+    pesticides, and to strengthen organic farming in order to protect
+    biodiversity and maintain food security.
+  - >-
+    Herpes simplex virus 1 (HSV-1) encodes Us3 protein kinase, which is critical
+    for viral pathogenicity in both mouse peripheral sites (e.g., eyes and
+    vaginas) and in the central nervous systems (CNS) of mice after intracranial
+    and peripheral inoculations, respectively. Whereas some Us3 substrates
+    involved in Us3 pathogenicity in peripheral sites have been reported, those
+    involved in Us3 pathogenicity in the CNS remain to be identified. We
+    recently reported that Us3 phosphorylated HSV-1 dUTPase (vdUTPase) at serine
+    187 (Ser-187) in infected cells, and this phosphorylation promoted viral
+    replication by regulating optimal enzymatic activity of vdUTPase. In the
+    present study, we show that the replacement of vdUTPase Ser-187 by alanine
+    (S187A) significantly reduced viral replication and virulence in the CNS of
+    mice following intracranial inoculation and that the phosphomimetic
+    substitution at vdUTPase Ser-187 in part restored the wild-type viral
+    replication and virulence. Interestingly, the S187A mutation in vdUTPase had
+    no effect on viral replication and pathogenic effects in the eyes and
+    vaginas of mice after ocular and vaginal inoculation, respectively.
+    Similarly, the enzyme-dead mutation in vdUTPase significantly reduced viral
+    replication and virulence in the CNS of mice after intracranial inoculation,
+    whereas the mutation had no effect on viral replication and pathogenic
+    effects in the eyes and vaginas of mice after ocular and vaginal
+    inoculation, respectively. These observations suggested that vdUTPase was
+    one of the Us3 substrates responsible for Us3 pathogenicity in the CNS and
+    that the CNS-specific virulence of HSV-1 involved strict regulation of
+    vdUTPase activity by Us3 phosphorylation.
+- source_sentence: >-
+    Load-dependent detachment and reattachment kinetics of kinesin-1, -2 and 3
+    motors
   sentences:
-  - Bidirectional cargo transport by kinesin and dynein is essential for cell viability
-    and defects are linked to neurodegenerative diseases. Computational modeling suggests
-    that the load-dependent off-rate is the strongest determinant of which motor 'wins'
-    a kinesin-dynein tug-of-war, and optical tweezer experiments find that the load-dependent
-    detachment sensitivity of transport kinesins is kinesin-3 > kinesin-2 > kinesin-1.
-    However, in reconstituted kinesin-dynein pairs vitro, all three kinesin families
-    compete nearly equally well against dynein. Modeling and experiments have confirmed
-    that vertical forces inherent to the large trapping beads enhance kinesin-1 dissociation
-    rates. In vivo, vertical forces are expected to range from negligible to dominant,
-    depending on cargo and microtubule geometries. To investigate the detachment and
-    reattachment kinetics of kinesin-1, 2 and 3 motors against loads oriented parallel
-    to the microtubule, we created a DNA tensiometer comprising a DNA entropic spring
-    attached to the microtubule on one end and a motor on the other. Kinesin dissociation
-    rates at stall were slower than detachment rates during unloaded runs, and the
-    complex reattachment kinetics were consistent with a weakly-bound 'slip' state
-    preceding detachment. Kinesin-3 behaviors under load suggested that long KIF1A
-    run lengths result from the concatenation of multiple short runs connected by
-    diffusive episodes. Stochastic simulations were able to recapitulate the load-dependent
-    detachment and reattachment kinetics for all three motors and provide direct comparison
-    of key transition rates between families. These results provide insight into how
-    kinesin-1, -2 and -3 families transport cargo in complex cellular geometries and
-    compete against dynein during bidirectional transport.
-  - 'AP-1 and AP-2 adaptor protein (AP) complexes mediate clathrin-dependent trafficking
-    at the trans-Golgi network (TGN) and the plasma membrane, respectively. Whereas
-    AP-1 is required for trafficking to plasma membrane and vacuoles, AP-2 mediates
-    endocytosis. These AP complexes consist of four subunits (adaptins): two large
-    subunits (β1 and γ for AP-1 and β2 and α for AP-2), a medium subunit μ, and a
-    small subunit σ. In general, adaptins are unique to each AP complex, with the
-    exception of β subunits that are shared by AP-1 and AP-2 in some invertebrates.
-    Here, we show that the two putative Arabidopsis thaliana AP1/2β adaptins co-assemble
-    with both AP-1 and AP-2 subunits and regulate exocytosis and endocytosis in root
-    cells, consistent with their dual localization at the TGN and plasma membrane.
-    Deletion of both β adaptins is lethal in plants. We identified a critical role
-    of β adaptins in pollen wall formation and reproduction, involving the regulation
-    of membrane trafficking in the tapetum and pollen germination. In tapetal cells,
-    β adaptins localize almost exclusively to the TGN and mediate exocytosis of the
-    plasma membrane transporters such as ATP-binding cassette (ABC)G9 and ABCG16.
-    This study highlights the essential role of AP1/2β adaptins in plants and their
-    specialized roles in specific cell types.'
-  - A single kinesin molecule can move "processively" along a microtubule for more
-    than 1 micrometer before detaching from it. The prevailing explanation for this
-    processive movement is the "walking model," which envisions that each of two motor
-    domains (heads) of the kinesin molecule binds coordinately to the microtubule.
-    This implies that each kinesin molecule must have two heads to "walk" and that
-    a single-headed kinesin could not move processively. Here, a motor-domain construct
-    of KIF1A, a single-headed kinesin superfamily protein, was shown to move processively
-    along the microtubule for more than 1 micrometer. The movement along the microtubules
+  - >-
+    Bidirectional cargo transport by kinesin and dynein is essential for cell
+    viability and defects are linked to neurodegenerative diseases.
+    Computational modeling suggests that the load-dependent off-rate is the
+    strongest determinant of which motor 'wins' a kinesin-dynein tug-of-war, and
+    optical tweezer experiments find that the load-dependent detachment
+    sensitivity of transport kinesins is kinesin-3 > kinesin-2 > kinesin-1.
+    However, in reconstituted kinesin-dynein pairs vitro, all three kinesin
+    families compete nearly equally well against dynein. Modeling and
+    experiments have confirmed that vertical forces inherent to the large
+    trapping beads enhance kinesin-1 dissociation rates. In vivo, vertical
+    forces are expected to range from negligible to dominant, depending on cargo
+    and microtubule geometries. To investigate the detachment and reattachment
+    kinetics of kinesin-1, 2 and 3 motors against loads oriented parallel to the
+    microtubule, we created a DNA tensiometer comprising a DNA entropic spring
+    attached to the microtubule on one end and a motor on the other. Kinesin
+    dissociation rates at stall were slower than detachment rates during
+    unloaded runs, and the complex reattachment kinetics were consistent with a
+    weakly-bound 'slip' state preceding detachment. Kinesin-3 behaviors under
+    load suggested that long KIF1A run lengths result from the concatenation of
+    multiple short runs connected by diffusive episodes. Stochastic simulations
+    were able to recapitulate the load-dependent detachment and reattachment
+    kinetics for all three motors and provide direct comparison of key
+    transition rates between families. These results provide insight into how
+    kinesin-1, -2 and -3 families transport cargo in complex cellular geometries
+    and compete against dynein during bidirectional transport.
+  - >-
+    AP-1 and AP-2 adaptor protein (AP) complexes mediate clathrin-dependent
+    trafficking at the trans-Golgi network (TGN) and the plasma membrane,
+    respectively. Whereas AP-1 is required for trafficking to plasma membrane
+    and vacuoles, AP-2 mediates endocytosis. These AP complexes consist of four
+    subunits (adaptins): two large subunits (β1 and γ for AP-1 and β2 and α for
+    AP-2), a medium subunit μ, and a small subunit σ. In general, adaptins are
+    unique to each AP complex, with the exception of β subunits that are shared
+    by AP-1 and AP-2 in some invertebrates. Here, we show that the two putative
+    Arabidopsis thaliana AP1/2β adaptins co-assemble with both AP-1 and AP-2
+    subunits and regulate exocytosis and endocytosis in root cells, consistent
+    with their dual localization at the TGN and plasma membrane. Deletion of
+    both β adaptins is lethal in plants. We identified a critical role of β
+    adaptins in pollen wall formation and reproduction, involving the regulation
+    of membrane trafficking in the tapetum and pollen germination. In tapetal
+    cells, β adaptins localize almost exclusively to the TGN and mediate
+    exocytosis of the plasma membrane transporters such as ATP-binding cassette
+    (ABC)G9 and ABCG16. This study highlights the essential role of AP1/2β
+    adaptins in plants and their specialized roles in specific cell types.
+  - >-
+    A single kinesin molecule can move "processively" along a microtubule for
+    more than 1 micrometer before detaching from it. The prevailing explanation
+    for this processive movement is the "walking model," which envisions that
+    each of two motor domains (heads) of the kinesin molecule binds coordinately
+    to the microtubule. This implies that each kinesin molecule must have two
+    heads to "walk" and that a single-headed kinesin could not move
+    processively. Here, a motor-domain construct of KIF1A, a single-headed
+    kinesin superfamily protein, was shown to move processively along the
+    microtubule for more than 1 micrometer. The movement along the microtubules
     was stochastic and fitted a biased Brownian-movement model.
-- source_sentence: Phylogenetic analysis of mitochondrial genes in Macquarie perch
-    from three river basins
+- source_sentence: >-
+    Phylogenetic analysis of mitochondrial genes in Macquarie perch from three
+    river basins
   sentences:
-  - Sedentary behavior is an emerging risk factor for cardiovascular disease (CVD)
-    and may be particularly relevant to the cardiovascular health of older adults.
-    This scoping review describes the existing literature examining the prevalence
-    of sedentary time in older adults with CVD and the association of sedentary behavior
-    with cardiovascular risk in older adults. We found that older adults with CVD
-    spend >75 % of their waking day sedentary, and that sedentary time is higher among
-    older adults with CVD than among older adults without CVD. High sedentary behavior
-    is consistently associated with worse cardiac lipid profiles and increased cardiac
-    risk scores in older adults; the associations of sedentary behavior with blood
-    pressure, CVD incidence, and CVD-related mortality among older adults are less
-    clear. Future research with larger sample sizes using validated methods to measure
-    sedentary behavior are needed to clarify the association between sedentary behavior
+  - >-
+    Sedentary behavior is an emerging risk factor for cardiovascular disease
+    (CVD) and may be particularly relevant to the cardiovascular health of older
+    adults. This scoping review describes the existing literature examining the
+    prevalence of sedentary time in older adults with CVD and the association of
+    sedentary behavior with cardiovascular risk in older adults. We found that
+    older adults with CVD spend >75 % of their waking day sedentary, and that
+    sedentary time is higher among older adults with CVD than among older adults
+    without CVD. High sedentary behavior is consistently associated with worse
+    cardiac lipid profiles and increased cardiac risk scores in older adults;
+    the associations of sedentary behavior with blood pressure, CVD incidence,
+    and CVD-related mortality among older adults are less clear. Future research
+    with larger sample sizes using validated methods to measure sedentary
+    behavior are needed to clarify the association between sedentary behavior
     and cardiovascular outcomes in older adults.
-  - An improved Bayesian method is presented for estimating phylogenetic trees using
-    DNA sequence data. The birth-death process with species sampling is used to specify
-    the prior distribution of phylogenies and ancestral speciation times, and the
-    posterior probabilities of phylogenies are used to estimate the maximum posterior
-    probability (MAP) tree. Monte Carlo integration is used to integrate over the
-    ancestral speciation times for particular trees. A Markov Chain Monte Carlo method
-    is used to generate the set of trees with the highest posterior probabilities.
-    Methods are described for an empirical Bayesian analysis, in which estimates of
-    the speciation and extinction rates are used in calculating the posterior probabilities,
-    and a hierarchical Bayesian analysis, in which these parameters are removed from
-    the model by an additional integration. The Markov Chain Monte Carlo method avoids
-    the requirement of our earlier method for calculating MAP trees to sum over all
-    possible topologies (which limited the number of taxa in an analysis to about
-    five). The methods are applied to analyze DNA sequences for nine species of primates,
-    and the MAP tree, which is identical to a maximum-likelihood estimate of topology,
-    has a probability of approximately 95%.
-  - 'Genetic variation in mitochondrial genes could underlie metabolic adaptations
-    because mitochondrially encoded proteins are directly involved in a pathway supplying
-    energy to metabolism. Macquarie perch from river basins exposed to different climates
-    differ in size and growth rate, suggesting potential presence of adaptive metabolic
-    differences. We used complete mitochondrial genome sequences to build a phylogeny,
-    estimate lineage divergence times and identify signatures of purifying and positive
-    selection acting on mitochondrial genes for 25 Macquarie perch from three basins:
-    Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin
-    (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient
-    speciation previously inferred from differentiation in allozymes, microsatellites
-    and mitochondrial control region. The estimated time of lineage divergence suggested
-    an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB,
-    followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence
-    estimates are more recent than previous ones. Our analyses suggested that evolutionary
-    drivers differed between inland MDB and coastal HNB. In the cooler and more climatically
-    variable MDB, mitogenomes evolved under strong purifying selection, whereas in
-    the warmer and more climatically stable HNB, purifying selection was relaxed.
-    Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S
-    ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations
-    and a codon (ATP6'
+  - >-
+    An improved Bayesian method is presented for estimating phylogenetic trees
+    using DNA sequence data. The birth-death process with species sampling is
+    used to specify the prior distribution of phylogenies and ancestral
+    speciation times, and the posterior probabilities of phylogenies are used to
+    estimate the maximum posterior probability (MAP) tree. Monte Carlo
+    integration is used to integrate over the ancestral speciation times for
+    particular trees. A Markov Chain Monte Carlo method is used to generate the
+    set of trees with the highest posterior probabilities. Methods are described
+    for an empirical Bayesian analysis, in which estimates of the speciation and
+    extinction rates are used in calculating the posterior probabilities, and a
+    hierarchical Bayesian analysis, in which these parameters are removed from
+    the model by an additional integration. The Markov Chain Monte Carlo method
+    avoids the requirement of our earlier method for calculating MAP trees to
+    sum over all possible topologies (which limited the number of taxa in an
+    analysis to about five). The methods are applied to analyze DNA sequences
+    for nine species of primates, and the MAP tree, which is identical to a
+    maximum-likelihood estimate of topology, has a probability of approximately
+    95%.
+  - >-
+    Genetic variation in mitochondrial genes could underlie metabolic
+    adaptations because mitochondrially encoded proteins are directly involved
+    in a pathway supplying energy to metabolism. Macquarie perch from river
+    basins exposed to different climates differ in size and growth rate,
+    suggesting potential presence of adaptive metabolic differences. We used
+    complete mitochondrial genome sequences to build a phylogeny, estimate
+    lineage divergence times and identify signatures of purifying and positive
+    selection acting on mitochondrial genes for 25 Macquarie perch from three
+    basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and
+    Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades,
+    supporting incipient speciation previously inferred from differentiation in
+    allozymes, microsatellites and mitochondrial control region. The estimated
+    time of lineage divergence suggested an early- to mid-Pleistocene split
+    between SB and the common ancestor of HNB+MDB, followed by mid-to-late
+    Pleistocene splitting between HNB and MDB. These divergence estimates are
+    more recent than previous ones. Our analyses suggested that evolutionary
+    drivers differed between inland MDB and coastal HNB. In the cooler and more
+    climatically variable MDB, mitogenomes evolved under strong purifying
+    selection, whereas in the warmer and more climatically stable HNB, purifying
+    selection was relaxed. Evidence for relaxed selection in the HNB includes
+    elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of
+    potentially mildly deleterious mutations and a codon (ATP6
 pipeline_tag: sentence-similarity
 library_name: sentence-transformers
+license: mit
 ---
 
 # SentenceTransformer based on thenlper/gte-base