cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25549/uschist-ouc12575663
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-ouc12575699
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-ouc12575831
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-ouc12575748
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-c104-283746
title: Unidentified young man, USC Trustee Conferences, Calif., 2007-2008

description: 6 photographs on an unidentified young man, Trustee Conferences, California, USA, 2007 March 31 (La Quinta Resort, La Quinta) (#414-#415) and 2008 March 29 (Westin Mission Hills Resort, Rancho Mirage) (#333-#336).
DOI: 10.25549/uschist-c104-284447
title: USC trustee Ronnie C. Chan & his wife, 2005 & 2007-2008

description: 7 photographs of University of Southern California trustee, Ronnie C. Chan, and his wife, 2005 February 23 (#146), 2007 November 7 (#21), and 2008 March 29 (Westin Mission Hills Resort, Rancho Mirage, California, USA) (#328-#329).
DOI: 10.25549/uschist-c104-285999
title: USC president Steven Sample & his wife Kathryn, Trustee Conferences, 2003-2005, 2007-2008

description: 27 photographs of University of Southern California president (1991-2010), Steven Sample, and his wife Kathryn, Trustee Conferences, California, USA, 2003 April 11 (#1-#7), 2004 April 1 (#17-#22), 2005 April (#86-#90), 2007 March 31 (La Quinta Resort, La Quinta) (#294-#299), and 2008 March 29 (Westin Mission Hills Resort, Rancho Mirage) (#347-#349).
DOI: 10.25549/uschist-c104-286000
title: USC president Steven Sample & his wife Kathryn, Trustee Conferences, 2003-2005, 2007-2008

description: 27 photographs of University of Southern California president (1991-2010), Steven Sample, and his wife Kathryn, Trustee Conferences, California, USA, 2003 April 11 (#1-#7), 2004 April 1 (#17-#22), 2005 April (#86-#90), 2007 March 31 (La Quinta Resort, La Quinta) (#294-#299), and 2008 March 29 (Westin Mission Hills Resort, Rancho Mirage) (#347-#349).
DOI: 10.25549/uschist-c104-286001
title: USC president Steven Sample & his wife Kathryn, Trustee Conferences, 2003-2005, 2007-2008

description: 27 photographs of University of Southern California president (1991-2010), Steven Sample, and his wife Kathryn, Trustee Conferences, California, USA, 2003 April 11 (#1-#7), 2004 April 1 (#17-#22), 2005 April (#86-#90), 2007 March 31 (La Quinta Resort, La Quinta) (#294-#299), and 2008 March 29 (Westin Mission Hills Resort, Rancho Mirage) (#347-#349).
DOI: 10.25549/uschist-ouc12575840
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-ouc12576050
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-ouc12576061
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-ouc12575847
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-ouc12575744
title: Entertainment, USC Trustee Conference, La Quinta, Calif., 2007

description: 103 photographs of a musical stage play at University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2007 March 31.
DOI: 10.25549/uschist-c104-285663
title: USC events executive director Jim Hooker, Trustee Conference, Calif., 2008

description: 12 photographs of University of Southern California executive director of protocol and university events, Jim Hooker, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 29.
DOI: 10.25549/uschist-c104-285664
title: USC events executive director Jim Hooker, Trustee Conference, Calif., 2008

description: 12 photographs of University of Southern California executive director of protocol and university events, Jim Hooker, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 29.
DOI: 10.25549/uschist-c104-285666
title: USC events executive director Jim Hooker, Trustee Conference, Calif., 2008

description: 12 photographs of University of Southern California executive director of protocol and university events, Jim Hooker, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 29.
DOI: 10.25549/uschist-c104-284691
title: USC trustee Raymond Watt & his wife Gwendolyn, before 1998, 2004-2005, 2007-2008

description: 19 photographs of University of Southern California trustee (1968-2009), Raymond A. Watt, and his wife, Gwendolyn, before 1998 (#131), 2004 April 1 (Trustee Conference) (#18-#21), 2005 April (Trustee Conference) (#32-#33), 2007 March 31 (Trustee Conference, La Quinta Resort, La Quinta, California, USA) (#273-#277), and 2008 March 29 (Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA) (#12-#18).
DOI: 10.25549/uschist-c104-284693
title: USC trustee Raymond Watt & his wife Gwendolyn, before 1998, 2004-2005, 2007-2008

description: 19 photographs of University of Southern California trustee (1968-2009), Raymond A. Watt, and his wife, Gwendolyn, before 1998 (#131), 2004 April 1 (Trustee Conference) (#18-#21), 2005 April (Trustee Conference) (#32-#33), 2007 March 31 (Trustee Conference, La Quinta Resort, La Quinta, California, USA) (#273-#277), and 2008 March 29 (Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA) (#12-#18).
DOI: 10.15468/dl.zscjrd
title: Occurrence Download

description: A dataset containing 54081 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anguilla rostrata",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 54081 records from 147 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030571-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18675671
title: Open Benchmark Dataset for Enzymatic Q–K Crosslink Identification by LC–MS/MS

description: This repository contains two LC–MS/MS raw data files (and .mgf versions if needed), associated search parameters, and curated FASTA databases generated from purified fibrinogen clots crosslinked by endogenous FXIIIa or recombinant transglutaminase 2 (TG2). These samples represent a controlled benchmark system for evaluating crosslink-mass spectrometry (XL-MS) software performance on non-cleavable enzymatic Q–K isopeptide bonds. Unlike conventional chemical crosslinkers, these transglutaminase-mediated crosslinks are zero-length modifications formed by ammonia (NH₃) loss, creating unique challenges for false discovery control and site assignment. The datasets are provided to enable transparent, community-driven comparison of XL search engines and to advance methodological development in enzymatic crosslink identification.
description: Search parameters:

MS1 tolerance: 10 ppm

MS2 tolerance: 20 ppm

Isotope error: 0, +1, +2

precursor: no filtering (if needed +2 to +8 - all are likely 3+ and above)

Fragmentation: HCD

Orbitrap MS2

 

Enzyme: Trypsin

Max missed cleavages: 3

Minimum peptide length: 5 amino acids

Maximum peptide length: 60 amino acids

Minimum chain mass: 500 Da

Maximum chain mass: 6000 Da

 

Fixed modification

Carbamidomethyl (Cys): +57.021464 Da

Variable modification

Oxidation (Met): +15.994915 Da

Maximum variable modifications per peptide: 3

 

If software creates its own decoys:

Use: Fibrin_medium.fasta

If software requires external decoys:

Use: Fibrin_medium_comb_rever.fasta

Reverse entries labeled with prefix: "REVERSE"

If search exceeds 24 hours or repeatedly fails:

Use fallback database: Fibrin_small.fasta

 

XL information

Crosslink Name: QKiso

Reactive Sites

Site 1: Q (Glutamine)

Site 2: K (Lysine)

Q–K only (no Q–Q or K–K if software allows restriction)

Crosslink Mass

−17.02654909 Da

Elemental composition: –NH₃, (N–1 H–3), N(-1)H(-3)

Dead-end / Mono-links Not considered

No hydrolyzed forms, etc.

 

result filter FDR < 0.05 (5%)

output: CSM - total crosslink spectral matches (.csv or similar)

peptide1, peptide2, site1, site2, prot1, prot2, run and scan# (ideally), score1, score2, etc

 

For comparison purposes:

Peptide1 (Protein1) should correspond to the Q-site peptide

Peptide2 (Protein2) should correspond to the K-site peptide

Please reorder accordingly before submission. (it would be helpful if data is delivered in this format:-).

In addition please provide:

Search parameter file (if available)

Full search log (or approx. time of run)

Software version number

Decoy strategy description (reverse, shuffled, target-decoy concatenated, etc.)
DOI: 10.5281/zenodo.18675670
title: Open Benchmark Dataset for Enzymatic Q–K Crosslink Identification by LC–MS/MS

description: This repository contains two LC–MS/MS raw data files (and .mgf versions if needed), associated search parameters, and curated FASTA databases generated from purified fibrinogen clots crosslinked by endogenous FXIIIa or recombinant transglutaminase 2 (TG2). These samples represent a controlled benchmark system for evaluating crosslink-mass spectrometry (XL-MS) software performance on non-cleavable enzymatic Q–K isopeptide bonds. Unlike conventional chemical crosslinkers, these transglutaminase-mediated crosslinks are zero-length modifications formed by ammonia (NH₃) loss, creating unique challenges for false discovery control and site assignment. The datasets are provided to enable transparent, community-driven comparison of XL search engines and to advance methodological development in enzymatic crosslink identification.
description: Search parameters:

MS1 tolerance: 10 ppm

MS2 tolerance: 20 ppm

Isotope error: 0, +1, +2

precursor: no filtering (if needed +2 to +8 - all are likely 3+ and above)

Fragmentation: HCD

Orbitrap MS2

 

Enzyme: Trypsin

Max missed cleavages: 3

Minimum peptide length: 5 amino acids

Maximum peptide length: 60 amino acids

Minimum chain mass: 500 Da

Maximum chain mass: 6000 Da

 

Fixed modification

Carbamidomethyl (Cys): +57.021464 Da

Variable modification

Oxidation (Met): +15.994915 Da

Maximum variable modifications per peptide: 3

 

If software creates its own decoys:

Use: Fibrin_medium.fasta

If software requires external decoys:

Use: Fibrin_medium_comb_rever.fasta

Reverse entries labeled with prefix: "REVERSE"

If search exceeds 24 hours or repeatedly fails:

Use fallback database: Fibrin_small.fasta

 

XL information

Crosslink Name: QKiso

Reactive Sites

Site 1: Q (Glutamine)

Site 2: K (Lysine)

Q–K only (no Q–Q or K–K if software allows restriction)

Crosslink Mass

−17.02654909 Da

Elemental composition: –NH₃, (N–1 H–3), N(-1)H(-3)

Dead-end / Mono-links Not considered

No hydrolyzed forms, etc.

 

result filter FDR < 0.05 (5%)

output: CSM - total crosslink spectral matches (.csv or similar)

peptide1, peptide2, site1, site2, prot1, prot2, run and scan# (ideally), score1, score2, etc

 

For comparison purposes:

Peptide1 (Protein1) should correspond to the Q-site peptide

Peptide2 (Protein2) should correspond to the K-site peptide

Please reorder accordingly before submission. (it would be helpful if data is delivered in this format:-).

In addition please provide:

Search parameter file (if available)

Full search log (or approx. time of run)

Software version number

Decoy strategy description (reverse, shuffled, target-decoy concatenated, etc.)
DOI: 10.5281/zenodo.15732465
title: Raw MS data for manuscript "Rubisco kinetic acclimation at the holoenzyme level"
DOI: 10.5281/zenodo.15732466
title: Raw MS data for manuscript "Rubisco kinetic acclimation at the holoenzyme level"
DOI: 10.25549/uschist-c104-288500
title: Sample presents commendation to Slavkin, Trustee Conference, Calif., 2009

description: 83 photographs of University of Southern California president Steven Sample and trustee Edward Roski presenting commendation to the school of dentistry dean (2000-2008), Harold Slavkin, USC Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2009 April 3. Also present is Slavkin's wife Lois. Photography by Anne Westfall (124 series).
DOI: 10.25549/uschist-c104-288501
title: Sample presents commendation to Slavkin, Trustee Conference, Calif., 2009

description: 83 photographs of University of Southern California president Steven Sample and trustee Edward Roski presenting commendation to the school of dentistry dean (2000-2008), Harold Slavkin, USC Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2009 April 3. Also present is Slavkin's wife Lois. Photography by Anne Westfall (124 series).
DOI: 10.5281/zenodo.18705739
title: Amyloid databases list

description: The database was developed by BioGenies team. If you want to get to know us and our projects visit our webpage BioGenies.

This website accompanies our publication:

Iglesias V, Chilimoniuk J, Pintado-Grima C, Bárcenas O, Ventura S, Burdukiewicz M (2024). “Aggregating Amyloid Resources: A Comprehensive Review of Databases on Amyloid-like Aggregation.” Computational and Structural Biotechnology Journal. ISSN 2001-0370, doi:10.1016/j.csbj.2024.10.047, https://doi.org/10.1016/j.csbj.2024.10.047, <2024-11-05>
DOI: 10.5281/zenodo.18705738
title: Amyloid databases list

description: The database was developed by BioGenies team. If you want to get to know us and our projects visit our webpage BioGenies.

This website accompanies our publication:

Iglesias V, Chilimoniuk J, Pintado-Grima C, Bárcenas O, Ventura S, Burdukiewicz M (2024). “Aggregating Amyloid Resources: A Comprehensive Review of Databases on Amyloid-like Aggregation.” Computational and Structural Biotechnology Journal. ISSN 2001-0370, doi:10.1016/j.csbj.2024.10.047, https://doi.org/10.1016/j.csbj.2024.10.047, <2024-11-05>
DOI: 10.25549/uschist-c104-282463
title: Musicians, USC Trustee Conference, Calif., 2008 March 28

description: 110 photographs of musical performers at University of Southern California Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, first night, 2008 March 28. Pictured are: Steven Sample, Aaron Serfaty.
DOI: 10.25549/uschist-c104-282468
title: Musicians, USC Trustee Conference, Calif., 2008 March 28

description: 110 photographs of musical performers at University of Southern California Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, first night, 2008 March 28. Pictured are: Steven Sample, Aaron Serfaty.
DOI: 10.34740/kaggle/dsv/14894115
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.25549/uschist-c104-282470
title: Musicians, USC Trustee Conference, Calif., 2008 March 28

description: 110 photographs of musical performers at University of Southern California Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, first night, 2008 March 28. Pictured are: Steven Sample, Aaron Serfaty.
DOI: 10.25549/uschist-c104-283041
title: Sample presents commendation to Laemmle, Trustee Conference, Calif., 2008

description: 12 photographs of University of Southern California president Steven Sample presenting commendation to dean of religious live, Susan Laemmle, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 28. Also present is Laemmle's husband John Antignas.
DOI: 10.25549/uschist-c104-288502
title: Sample presents commendation to Slavkin, Trustee Conference, Calif., 2009

description: 83 photographs of University of Southern California president Steven Sample and trustee Edward Roski presenting commendation to the school of dentistry dean (2000-2008), Harold Slavkin, USC Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2009 April 3. Also present is Slavkin's wife Lois. Photography by Anne Westfall (124 series).
DOI: 10.25549/uschist-c104-288523
title: Sample presents commendation to Slavkin, Trustee Conference, Calif., 2009

description: 83 photographs of University of Southern California president Steven Sample and trustee Edward Roski presenting commendation to the school of dentistry dean (2000-2008), Harold Slavkin, USC Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2009 April 3. Also present is Slavkin's wife Lois. Photography by Anne Westfall (124 series).
DOI: 10.25549/uschist-c104-288524
title: Sample presents commendation to Slavkin, Trustee Conference, Calif., 2009

description: 83 photographs of University of Southern California president Steven Sample and trustee Edward Roski presenting commendation to the school of dentistry dean (2000-2008), Harold Slavkin, USC Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2009 April 3. Also present is Slavkin's wife Lois. Photography by Anne Westfall (124 series).
DOI: 10.25549/uschist-c104-288739
title: Venue, USC Trustee Conference, La Quinta, Calif., 2009 April 3-4

description: 57 photographs of venue for the University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2009 April 3-4. Photography by Anne Westfall.
DOI: 10.25549/uschist-c104-288744
title: Venue, USC Trustee Conference, La Quinta, Calif., 2009 April 3-4

description: 57 photographs of venue for the University of Southern California Trustee Conference, La Quinta Resort, La Quinta, California, USA, 2009 April 3-4. Photography by Anne Westfall.
DOI: 10.25549/uschist-c104-283051
title: Sample presents commendation to Laemmle, Trustee Conference, Calif., 2008

description: 12 photographs of University of Southern California president Steven Sample presenting commendation to dean of religious live, Susan Laemmle, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 28. Also present is Laemmle's husband John Antignas.
DOI: 10.5281/zenodo.18705682
title: Data used in "Energy gap of quantum spin glasses: a projection quantum Monte Carlo study"

description: README - Data Archive for "Energy gap of quantum spin glasses: a projection quantum Monte Carlo study"

Overview--------This archive (data.zip) contains the numerical data used to generate all figures in the accompanying manuscript. The data are organized into folders according to the figure labels in the main text, end matter, and supplemental material. Each folder contains plain-text .dat files with columns representing the variables necessary to reproduce the plots.

Folder Structure----------------- fig1-4       : Data for figures 1 through 4 in the main text.- figEM6-8     : Data for figures 6 through 8 in the End Matter.- figSM1-4     : Data for figures 1 through 4 in the Supplemental Material.

Data Format-----------Each .dat file typically contains three columns:

1. The independent variable (x-axis).2. The dependent variable (y-axis).3. The uncertainty (error bar) associated with the y-values.

All values are in the units specified in the manuscript. Columns are whitespace-separated and can be loaded directly using standard data analysis tools (Python, Gnuplot, Mathematica, etc.).

Inset Figures-------------For figures that include an inset, the corresponding data are provided in separate files with names clearly indicating that they correspond to the inset (e.g., "inset_<figure_name>.dat"). The same column structure applies.

Usage-------------The files can be used to reproduce the plots presented in the manuscript and perform further analysis or cross-checks.
DOI: 10.5281/zenodo.18705683
title: Data used in "Energy gap of quantum spin glasses: a projection quantum Monte Carlo study"

description: README - Data Archive for "Energy gap of quantum spin glasses: a projection quantum Monte Carlo study"

Overview--------This archive (data.zip) contains the numerical data used to generate all figures in the accompanying manuscript. The data are organized into folders according to the figure labels in the main text, end matter, and supplemental material. Each folder contains plain-text .dat files with columns representing the variables necessary to reproduce the plots.

Folder Structure----------------- fig1-4       : Data for figures 1 through 4 in the main text.- figEM6-8     : Data for figures 6 through 8 in the End Matter.- figSM1-4     : Data for figures 1 through 4 in the Supplemental Material.

Data Format-----------Each .dat file typically contains three columns:

1. The independent variable (x-axis).2. The dependent variable (y-axis).3. The uncertainty (error bar) associated with the y-values.

All values are in the units specified in the manuscript. Columns are whitespace-separated and can be loaded directly using standard data analysis tools (Python, Gnuplot, Mathematica, etc.).

Inset Figures-------------For figures that include an inset, the corresponding data are provided in separate files with names clearly indicating that they correspond to the inset (e.g., "inset_<figure_name>.dat"). The same column structure applies.

Usage-------------The files can be used to reproduce the plots presented in the manuscript and perform further analysis or cross-checks.
DOI: 10.25549/uschist-c104-285370
title: Sample presents commendation to Kreditor, Trustee Conference, Calif., 2008

description: 12 photographs of University of Southern California president Steven Sample presenting commendation to vice president of university advancement, Alan Kreditor, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 28. Also present is Kreditor's wife Marcia.
DOI: 10.25549/uschist-c104-285372
title: Sample presents commendation to Kreditor, Trustee Conference, Calif., 2008

description: 12 photographs of University of Southern California president Steven Sample presenting commendation to vice president of university advancement, Alan Kreditor, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 28. Also present is Kreditor's wife Marcia.
DOI: 10.25549/uschist-c104-282284
title: Sample presents commendation to Dougherty, Trustee Conference, Calif., 2008

description: 11 photographs of University of Southern California president Steven Sample presenting commendation to senior vice president for finance and chief financial officer, Dennis Dougherty, USC Trustee Conference, Westin Mission Hills Resort, Rancho Mirage, California, USA, 2008 March 28. Also present is Dougherty's wife Shia Carol.