cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15701099
title: High-affinity probes for androgen receptor imaging: from cells and in silico modeling to whole-body fluorescent applications

description: Structural information in support of the manuscript

"High-affinity probes for androgen receptor imaging: from cells and in silico modeling to whole-body fluorescent applications"by Saheed A. Ayodeji1,2, Yaroslav Balytskyi3, Destina Unaegbu1,4, Allison Ingman1,2, Christopher V. Kelly3, Sheryl Roberts1,2*

1 Molecular Therapeutics Program, Oncology, Karmanos Cancer Institute, Detroit, MI, 48201, USA. 2 Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA. 3 Department of Physics and Astronomy, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI, 48202, USA.4 Department of Chemistry, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI, 48202, USA.

Included here are the structural details of androgen receptor (AR) variants, bound ligands, and the majority-voted ligand binding pocket.  AR variants include wild-type aa670-919 and clinically relevant AR mutants (F877L, T878A, H875Y, W742C, and F877L/T878A). Ligands include 5-dihydrotestosterone (DHT), metribolone, ARi-NH, ARi-488-FL, and ARi-650-FL. The unbound (APO) structures are also provided.

The joint structure prediction of the protein and ligand were calculated through Chai-1 (1). The ligand binding pocket was calculated by RAPID-Net (2). Further details are provided in the manuscript. 

A preprint of the manuscript is available on the ChemRxiv:https://chemrxiv.org/engage/chemrxiv/article-details/67c5bcfa81d2151a02e11171DOI: 10.26434/chemrxiv-2025-40bvk-v2

(1) Chai Discovery, Jacques Boitreaud, Jack Dent, Matthew McPartlon, Joshua Meier, Vinicius Reis, Alex Rogozhnikov, and Kevin Wu, "Chai-1: Decoding the molecular interactions of life" bioRxiv 2024.10.10.615955, DOI: 10.1101/2024.10.10.615955https://www.biorxiv.org/content/10.1101/2024.10.10.615955v2

(2) Yaroslav Balytskyi, Inna Hubenko, Alina Balytska, and Christopher V. Kelly, "Accurate Pocket Identification for Binding-Site-Agnostic Docking." arXiv 2025, 2502.02371, DOI:10.48550/arXiv.2502.02371https://arxiv.org/abs/2502.02371
DOI: 10.5281/zenodo.15701100
title: High-affinity probes for androgen receptor imaging: from cells and in silico modeling to whole-body fluorescent applications

description: Structural information in support of the manuscript

"High-affinity probes for androgen receptor imaging: from cells and in silico modeling to whole-body fluorescent applications"by Saheed A. Ayodeji1,2, Yaroslav Balytskyi3, Destina Unaegbu1,4, Allison Ingman1,2, Christopher V. Kelly3, Sheryl Roberts1,2*

1 Molecular Therapeutics Program, Oncology, Karmanos Cancer Institute, Detroit, MI, 48201, USA. 2 Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA. 3 Department of Physics and Astronomy, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI, 48202, USA.4 Department of Chemistry, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI, 48202, USA.

Included here are the structural details of androgen receptor (AR) variants, bound ligands, and the majority-voted ligand binding pocket.  AR variants include wild-type aa670-919 and clinically relevant AR mutants (F877L, T878A, H875Y, W742C, and F877L/T878A). Ligands include 5-dihydrotestosterone (DHT), metribolone, ARi-NH, ARi-488-FL, and ARi-650-FL. The unbound (APO) structures are also provided.

The joint structure prediction of the protein and ligand were calculated through Chai-1 (1). The ligand binding pocket was calculated by RAPID-Net (2). Further details are provided in the manuscript. 

A preprint of the manuscript is available on the ChemRxiv:https://chemrxiv.org/engage/chemrxiv/article-details/67c5bcfa81d2151a02e11171DOI: 10.26434/chemrxiv-2025-40bvk-v2

(1) Chai Discovery, Jacques Boitreaud, Jack Dent, Matthew McPartlon, Joshua Meier, Vinicius Reis, Alex Rogozhnikov, and Kevin Wu, "Chai-1: Decoding the molecular interactions of life" bioRxiv 2024.10.10.615955, DOI: 10.1101/2024.10.10.615955https://www.biorxiv.org/content/10.1101/2024.10.10.615955v2

(2) Yaroslav Balytskyi, Inna Hubenko, Alina Balytska, and Christopher V. Kelly, "Accurate Pocket Identification for Binding-Site-Agnostic Docking." arXiv 2025, 2502.02371, DOI:10.48550/arXiv.2502.02371https://arxiv.org/abs/2502.02371
DOI: 10.15468/dl.cx74rm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neolamprologus furcifer (Boulenger, 1898)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((7.2484 2.1771,7.0894 2.0599,7.744 2.0599,7.6712 2.1357,7.2484 2.1771))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058266-250525065834625/datasets/export for details.
DOI: 10.15468/dl.9naab2
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Museum of Comparative Zoology, Harvard University",
 "Geometry POLYGON((-83.13082 32.66498,-82.84678 33.91093,-78.40184 35.75853,-76.42902 38.79361,-76.75006 40.62988,-80.15822 39.28123,-82.64631 37.67624,-84.82245 36.68939,-86.27833 35.29976,-86.20074 34.01681,-85.97138 33.31861,-85.09908 33.4134,-83.13082 32.66498))",
 "TaxonKey is Nerodia sipedon (Linnaeus, 1758)"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058267-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.em2tyt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cylindrocapsa Reinsch, 1867",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.6306 -23.844,35.6007 -23.8125,35.6007 -24.0157,35.6306 -23.844))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058268-250525065834625/datasets/export for details.
DOI: 10.15468/dl.vww38p
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arceuthobium verticilliflora Engelm."
 ]
}

 The dataset includes 67 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058269-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e233586
title: Prevalence of Hearing Loss in the United States by Industry, 2000-2008

description: Background: Twenty-two million workers are exposed to hazardous noise in the United States. The purpose of this study is to estimate the prevalence of hearing loss among U.S. industries.\n\nMethods: We examined 2000–2008 audiograms for male and female workers ages 18–65, who had higher occupational noise exposures than the general population. Prevalence and adjusted prevalence ratios (PRs) for hearing loss were estimated and compared across industries.\n\nResults: In our sample, 18% of workers had hearing loss. When compared with the Couriers and Messengers industry sub-sector, workers employed in Mining (PR = 1.65, CI = 1.57–1.73), Wood Product Manufacturing (PR = 1.65, CL = 1.61– 1.70), Construction of Buildings (PR = 1.59, CI = 1.51–1.68), and Real Estate and Rental and Leasing (PR = 1.61, CL = 1.51–1.71) had higher risks for hearing loss.\n\nConclusions: Workers in the Mining, Manufacturing, and Construction industries need better engineering controls for noise and stronger hearing conservation strategies. More hearing loss research is also needed within traditional ‘‘low-risk’’ industries like Real Estate.
DOI: 10.3886/e233586v1
title: Prevalence of Hearing Loss in the United States by Industry, 2000-2008

description: Background: Twenty-two million workers are exposed to hazardous noise in the United States. The purpose of this study is to estimate the prevalence of hearing loss among U.S. industries.\n\nMethods: We examined 2000–2008 audiograms for male and female workers ages 18–65, who had higher occupational noise exposures than the general population. Prevalence and adjusted prevalence ratios (PRs) for hearing loss were estimated and compared across industries.\n\nResults: In our sample, 18% of workers had hearing loss. When compared with the Couriers and Messengers industry sub-sector, workers employed in Mining (PR = 1.65, CI = 1.57–1.73), Wood Product Manufacturing (PR = 1.65, CL = 1.61– 1.70), Construction of Buildings (PR = 1.59, CI = 1.51–1.68), and Real Estate and Rental and Leasing (PR = 1.61, CL = 1.51–1.71) had higher risks for hearing loss.\n\nConclusions: Workers in the Mining, Manufacturing, and Construction industries need better engineering controls for noise and stronger hearing conservation strategies. More hearing loss research is also needed within traditional ‘‘low-risk’’ industries like Real Estate.
DOI: 10.15468/dl.vumkp9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neolamprologus furcifer (Boulenger, 1898)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((1.1203 5.3273,1.1382 5.3438,1.1382 11.0599,-7.8618 11.0599,-7.8618 3.9537,-7.6185 3.8529,-5.722 4.551,-4.0045 4.7444,-1.8508 4.2719,0.3589 5.2679,1.1203 5.3273))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058270-250525065834625/datasets/export for details.
DOI: 10.15468/dl.tfkpb7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cylindrocystis Meneghini ex De Bary, 1858",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.0251 -31.3959,30.5701 -30.7329,30.5701 -28.5786,25.5395 -28.5786,25.5395 -32.9007,28.2048 -32.9007,28.5753 -32.6569,29.4902 -31.7517,30.0251 -31.3959))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058271-250525065834625/datasets/export for details.
DOI: 10.15468/dl.6gmf8e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neolamprologus furcifer (Boulenger, 1898)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((3.8924 37.4235,1.1382 37.0126,1.1382 29.0599,10.1382 29.0599,10.1382 37.8331,9.4029 37.7805,8.9557 38.0599,8.517 37.8538,8.3781 37.425,6.4409 37.5887,5.341 37.2123,4.8286 37.3907,3.8924 37.4235))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058272-250525065834625/datasets/export for details.
DOI: 10.3886/e233589
title: MicroRNA-Mediated KrÃ¼ppel-Like Factor 4 upregulation Induces Alternatively Activated Macrophage-Associated Markers and Chemokines Transcription in 4,4'-Methylene Diphenyl Diisocyanate Exposed Macrophages

description: Occupational exposure to 4,4â€™-methylene diphenyl diisocyanate (MDI), the most widely used monomeric diisocyanate (dNCO), is associated with occupational asthma (OA) development. Recruitment of immune cells to the lung microenvironment via secreted chemokines by alveolar macrophages may play a role during asthma pathogenesis. Our prior study identified that alternatively activated (M2) macrophage-associated markers and chemokines were induced by MDI/MDI-Glutathione (GSH)-mediated KrÃ¼ppel-Like Factor 4 (KLF4) upregulation in macrophages and induced chemotaxis abilities to naÃ¯ve T-cells and eosinophils; however, the underlying molecular mechanism(s) by which MDI upregulated KLF4 expression is unclear. Previously, we identified that two microRNAs (miRs) including hsa-miR-206-3p and hsa-miR-381-3p were significantly downregulated in MDI-GSH-exposed THP-1 macrophages. In silico analysis revealed that one hsa-miR-206-3p and two hsa-miR-381-3p predicted binding sites exist on the 3â€™ untranslated region (UTR) of KLF4 transcripts. We hypothesize that MDI/MDI-GSH exposure induces M2 macrophage-associated markers and chemokines through hsa-miR-206-3p/hsa-miR-381-3p mediated KLF4 upregulation in macrophages. The first aim of this study was to examine whether hsa-miR-206-3p/hsa-miR-381-3p regulates KLF4 expression in THP-1 macrophages through a posttranscriptional regulation mechanism. Our second aim was to determine whether hsa-miR-206-3p/hsa-miR-381-3p participates in KLF4-regulated M2 macrophage-associated markers and chemokines after MDI-exposure. After identifying the role of endogenous hsa-miR-206-3p/hsa-miR-381-3p in regulation of KLF4 transcription factor after MDI-exposure, we investigated the role of hsa-miR-206-3p/hsa-miR-381-3p in regulation of M2 macrophage-associated markers and chemokinesâ€™ expressions in relation to the exposure to MDI.<br>
DOI: 10.3886/e233589v1
title: MicroRNA-Mediated KrÃ¼ppel-Like Factor 4 upregulation Induces Alternatively Activated Macrophage-Associated Markers and Chemokines Transcription in 4,4'-Methylene Diphenyl Diisocyanate Exposed Macrophages

description: Occupational exposure to 4,4â€™-methylene diphenyl diisocyanate (MDI), the most widely used monomeric diisocyanate (dNCO), is associated with occupational asthma (OA) development. Recruitment of immune cells to the lung microenvironment via secreted chemokines by alveolar macrophages may play a role during asthma pathogenesis. Our prior study identified that alternatively activated (M2) macrophage-associated markers and chemokines were induced by MDI/MDI-Glutathione (GSH)-mediated KrÃ¼ppel-Like Factor 4 (KLF4) upregulation in macrophages and induced chemotaxis abilities to naÃ¯ve T-cells and eosinophils; however, the underlying molecular mechanism(s) by which MDI upregulated KLF4 expression is unclear. Previously, we identified that two microRNAs (miRs) including hsa-miR-206-3p and hsa-miR-381-3p were significantly downregulated in MDI-GSH-exposed THP-1 macrophages. In silico analysis revealed that one hsa-miR-206-3p and two hsa-miR-381-3p predicted binding sites exist on the 3â€™ untranslated region (UTR) of KLF4 transcripts. We hypothesize that MDI/MDI-GSH exposure induces M2 macrophage-associated markers and chemokines through hsa-miR-206-3p/hsa-miR-381-3p mediated KLF4 upregulation in macrophages. The first aim of this study was to examine whether hsa-miR-206-3p/hsa-miR-381-3p regulates KLF4 expression in THP-1 macrophages through a posttranscriptional regulation mechanism. Our second aim was to determine whether hsa-miR-206-3p/hsa-miR-381-3p participates in KLF4-regulated M2 macrophage-associated markers and chemokines after MDI-exposure. After identifying the role of endogenous hsa-miR-206-3p/hsa-miR-381-3p in regulation of KLF4 transcription factor after MDI-exposure, we investigated the role of hsa-miR-206-3p/hsa-miR-381-3p in regulation of M2 macrophage-associated markers and chemokinesâ€™ expressions in relation to the exposure to MDI.<br>
DOI: 10.3886/e233594v1
title: Total Inward Leakage (TIL) for Respiratory Protective Devices

description: Total inward leakage (TIL) is an estimate of the performance of a respirator, which is measured as the leakage of contaminants through the filter media and through the faceseal interface and exhalation valve of respiratory protective devices under laboratory conditions. Several test agents have been used to measure TIL in different countries. There is a lack of consensus on the most appropriate test method to measure TIL. The International Organization for Standardization (ISO) developed a standard (ISO, 2014) on the comparison of TIL measurement using sodium chloride (NaCl) and corn oil aerosols, and sulfur hexafluoride gas. A comparison of the TIL values between different methods will enable the selection of a relatively suitable method for measuring TIL. NIOSHâ€™s National Personal Protective Technology Laboratory (NPPTL) investigated the TIL values for respirators worn by test subjects exposed to NaCl and corn oil aerosols in two aerosol chambers side-by-side. Four air-purifying respirator categories, made
DOI: 10.15468/dl.m2hs8s
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cylindrocystis Meneghini ex De Bary, 1858",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.5701 -24.0715,25.5395 -24.0715,25.5395 -28.5786,30.5701 -28.5786,30.5701 -24.0715))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058273-250525065834625/datasets/export for details.
DOI: 10.15468/dl.hzbsbn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neolamprologus furcifer (Boulenger, 1898)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-7.2368 34.3499,-7.8618 34.0821,-7.8618 29.0599,1.1382 29.0599,1.1382 37.0126,1.0824 37.0043,-0.2178 36.3911,-1.3535 36.1755,-2.0167 35.582,-2.9629 35.9401,-3.4108 35.7059,-4.4085 35.6649,-4.8295 35.8931,-5.2547 36.4009,-6.1318 36.2488,-7.2368 34.3499))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058274-250525065834625/datasets/export for details.
DOI: 10.15468/dl.pjv68e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cylindrocystis Meneghini ex De Bary, 1858",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1332 -20.158,25.5395 -23.2724,25.5395 -24.0715,30.5701 -24.0715,30.5701 -20.3186,29.6496 -19.6123,28.947 -19.4003,28.1821 -19.4609,27.6072 -19.7214,27.1332 -20.158))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058275-250525065834625/datasets/export for details.
DOI: 10.3886/e233591
title: Efficacy of universal masking for source control and personal protection from simulated respiratory aerosols in a room

description: Masks block aerosols produced during coughs and exhalations (“source control”). Masks also slow and deflect cough and exhalation airflows, which changes the dispersion of aerosols. Factors such as the directions in which people are facing (orientation) and separation distance also affect aerosol dispersion. However, it is not clear how masking, orientation, and distance interact. We placed a respiratory aerosol simulator (“source”) and a breathing simulator (“recipient”) in a chamber and measured aerosol concentrations for different combinations of masking, orientation, and separation distance. When the simulators were front-to-front during coughing, masks reduced the 15-minute mean aerosol concentration at the recipient by 92% (p \u003c 0.0001) at 0.9 and 1.8 m separation. When the simulators were side-by-side, masks reduced the concentration by 81% at 0.9 m and 78% at 1.8 m (p \u003c 0.0001 for both). During breathing, masks reduced the aerosol concentration by 66% when front-to-front (p = 0.0056) and 76% when side-by-side (p \u003c 0.0001) at 0.9 m. Similar results were seen at 1.8 m. When the simulators were unmasked, changing the orientations from front-to-front to side-by-side reduced the cough aerosol concentration by 59% at 0.9 m and 60% at 1.8 m (p \u003c 0.0001 for both). When both simulators were masked, changing the orientations did not significantly change the concentration at either distance during coughing or breathing. Increasing the distance between the simulators from 0.9 m to 1.8 m during coughing reduced the aerosol concentration by 25% when no masks were worn (p \u003c 0.0001) but had little effect when both simulators were masked (4% decrease, p = 0.7090). During breathing, when neither simulator was masked, increasing the separation reduced the concentration by 13%, which approached significance (p = 0.0737), while the change was not significant when both source and recipient were masked (8% decrease, p = 0.3235). Our results suggest that universal masking reduces exposure to respiratory aerosol particles regardless of the orientation and separation distance between the source and recipient.