cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29196044.v1
title: SNP-associated differential methylation in <i>ARHGEF38</i>: insights into genetic-epigenetic interactions

description: Associations have been seen between suicide and differential DNA methylation, with one study showing significant hypomethylation of <i>ARHGEF38</i> in individuals with bipolar disorder who died by suicide. Our objective was to explore <i>ARHGEF38</i> methylation in individuals with bipolar disorder and a history of suicide attempt. With pyrosequencing, we looked at the previously identified region of interest in <i>ARHGEF38</i>. We investigated the methylation levels of three CpG sites in 47 individuals with bipolar disorder and a history of suicide attempt, 47 individuals with bipolar disorder without a history of suicide attempt, and 47 non-bipolar disorder controls. None of the CpG sites measured had an association between groups, although there were distinct clusters of differential methylation in each group. Applying genotypes of SNPs found in the region of interest, rs2121558 and rs1447093, these clusters showed stepwise methylation at each CpG site, regardless of phenotype. In this small sample size study, differential methylation in <i>ARHGEF38</i> was not associated with history of suicide attempt, failing to replicate findings from a related outcome, suicide death. However, we did provide evidence of SNP and DNA methylation interplay in this region. This highlights the relevance of considering genetics when interrogating epigenetic mechanisms. DNA methylation is a dynamic modification to DNA that changes throughout our lifetime due to a variety of extrinsic and intrinsic factors. This study aimed to investigate whether DNA methylation patterns in a gene previously associated with suicide death (<i>ARHGEF38</i>) was associated with a history of suicide attempts in individuals with bipolar disorder. To do this, we extracted DNA from whole blood samples from individuals with bipolar disorder (with and without a history of suicide attempts), and a control group without bipolar disorder. Using a targeted technique called pyrosequencing, we examined the methylation levels of three specific CpG sites within the <i>ARHGEF38</i> gene. This study found no significant differences in methylation levels between the groups at the three CpG sites analyzed. However, we did identify genetic variation close to the CpG sites that were associated with the identified DNA methylation patterns. This study did not replicate the previous finding that linked <i>ARHGEF38</i> to suicide death. Several differences between the previous study and this one may have influenced the negative finding, including the suicide phenotype, the tissue type, and the presence of genetic variation. This study is still notable as it highlights the complex interplay between genetic variants and DNA methylation patterns in epigenetic research.
DOI: 10.6084/m9.figshare.28939117
title: Selective chemical tracking of DNA methylomes in live cells

description: Selective chemical tracking of DNA methylomes in live cells
DOI: 10.6084/m9.figshare.28939117.v1
title: Selective chemical tracking of DNA methylomes in live cells

description: Selective chemical tracking of DNA methylomes in live cells
DOI: 10.6084/m9.figshare.28956132
title: Ubiquitin proteasome system (UPS): a crucial determinant of the epigenetic landscape in cancer

description: The ubiquitin proteasome system (UPS), comprising of ubiquitinases, deubiquitinases and 26S proteasome plays a significant role in directly or indirectly regulating epigenetic players. DNA-templated processes like replication, repair and transcription require chromatin decondensation to allow access to specific DNA sequence. A thorough survey of literary articles in PubMed database revealed that the UPS functions as a key regulator, determining the precise state of open and closed chromatin by influencing histones and histone modifiers through proteolytic or non-proteolytic means. However, a comprehensive understanding of how specific UPS components affect particular epigenetic pathways in response to environmental cues remains underexplored. This axis holds substantial potential for deciphering mechanisms of tumorigenesis. Although our current knowledge is limited, it can still guide the development of novel therapeutic strategies that can potentially bridge the gap between cancer chemotherapeutics in bench and bedside. The ubiquitin proteasome system (UPS) is responsible for managing proteins in the cell by tagging them with ubiquitin, which can change their function, location, or cause them to be broken down. This system also helps control how DNA is copied and how genes are activated by modifying histones – proteins that organize DNA. Although scientists know that UPS plays a role in cancer, they are still learning how it affects specific epigenetic processes. Gaining deeper insights could help develop more targeted and effective cancer treatments based on these protein–DNA interactions.
DOI: 10.6084/m9.figshare.28956132.v1
title: Ubiquitin proteasome system (UPS): a crucial determinant of the epigenetic landscape in cancer

description: The ubiquitin proteasome system (UPS), comprising of ubiquitinases, deubiquitinases and 26S proteasome plays a significant role in directly or indirectly regulating epigenetic players. DNA-templated processes like replication, repair and transcription require chromatin decondensation to allow access to specific DNA sequence. A thorough survey of literary articles in PubMed database revealed that the UPS functions as a key regulator, determining the precise state of open and closed chromatin by influencing histones and histone modifiers through proteolytic or non-proteolytic means. However, a comprehensive understanding of how specific UPS components affect particular epigenetic pathways in response to environmental cues remains underexplored. This axis holds substantial potential for deciphering mechanisms of tumorigenesis. Although our current knowledge is limited, it can still guide the development of novel therapeutic strategies that can potentially bridge the gap between cancer chemotherapeutics in bench and bedside. The ubiquitin proteasome system (UPS) is responsible for managing proteins in the cell by tagging them with ubiquitin, which can change their function, location, or cause them to be broken down. This system also helps control how DNA is copied and how genes are activated by modifying histones – proteins that organize DNA. Although scientists know that UPS plays a role in cancer, they are still learning how it affects specific epigenetic processes. Gaining deeper insights could help develop more targeted and effective cancer treatments based on these protein–DNA interactions.
DOI: 10.6084/m9.figshare.29196044
title: SNP-associated differential methylation in <i>ARHGEF38</i>: insights into genetic-epigenetic interactions

description: Associations have been seen between suicide and differential DNA methylation, with one study showing significant hypomethylation of <i>ARHGEF38</i> in individuals with bipolar disorder who died by suicide. Our objective was to explore <i>ARHGEF38</i> methylation in individuals with bipolar disorder and a history of suicide attempt. With pyrosequencing, we looked at the previously identified region of interest in <i>ARHGEF38</i>. We investigated the methylation levels of three CpG sites in 47 individuals with bipolar disorder and a history of suicide attempt, 47 individuals with bipolar disorder without a history of suicide attempt, and 47 non-bipolar disorder controls. None of the CpG sites measured had an association between groups, although there were distinct clusters of differential methylation in each group. Applying genotypes of SNPs found in the region of interest, rs2121558 and rs1447093, these clusters showed stepwise methylation at each CpG site, regardless of phenotype. In this small sample size study, differential methylation in <i>ARHGEF38</i> was not associated with history of suicide attempt, failing to replicate findings from a related outcome, suicide death. However, we did provide evidence of SNP and DNA methylation interplay in this region. This highlights the relevance of considering genetics when interrogating epigenetic mechanisms. DNA methylation is a dynamic modification to DNA that changes throughout our lifetime due to a variety of extrinsic and intrinsic factors. This study aimed to investigate whether DNA methylation patterns in a gene previously associated with suicide death (<i>ARHGEF38</i>) was associated with a history of suicide attempts in individuals with bipolar disorder. To do this, we extracted DNA from whole blood samples from individuals with bipolar disorder (with and without a history of suicide attempts), and a control group without bipolar disorder. Using a targeted technique called pyrosequencing, we examined the methylation levels of three specific CpG sites within the <i>ARHGEF38</i> gene. This study found no significant differences in methylation levels between the groups at the three CpG sites analyzed. However, we did identify genetic variation close to the CpG sites that were associated with the identified DNA methylation patterns. This study did not replicate the previous finding that linked <i>ARHGEF38</i> to suicide death. Several differences between the previous study and this one may have influenced the negative finding, including the suicide phenotype, the tissue type, and the presence of genetic variation. This study is still notable as it highlights the complex interplay between genetic variants and DNA methylation patterns in epigenetic research.
DOI: 10.5281/zenodo.15600302
title: Mertens conjecture proof

description: This paper addresses the disproof and reinterpretation of the Mertens Conjecture, which originally claimed that the summatory Möbius function M(n) satisfies |M(n)| < √n for all n. While the original conjecture was disproven in 1985, this paper presents a refined inequality that aligns with analytic number theory and modern bounds. We propose that M(n) remains constrained by a modified bound: |M(n)| < c·√n·log n, for some constant c. This formulation respects the known counterexamples while preserving the core intuition behind the original claim, offering a new lens on Möbius oscillation and zeta function behavior.
DOI: 10.5281/zenodo.15600303
title: Mertens conjecture proof

description: This paper addresses the disproof and reinterpretation of the Mertens Conjecture, which originally claimed that the summatory Möbius function M(n) satisfies |M(n)| < √n for all n. While the original conjecture was disproven in 1985, this paper presents a refined inequality that aligns with analytic number theory and modern bounds. We propose that M(n) remains constrained by a modified bound: |M(n)| < c·√n·log n, for some constant c. This formulation respects the known counterexamples while preserving the core intuition behind the original claim, offering a new lens on Möbius oscillation and zeta function behavior.
DOI: 10.71486/2e41-pw44
title: Dataset of the work "UBU-Polymers Research Group 03062025"

description: The dataset contains all raw data of the work "Intrinsically Colored Magenta Aramids with Improved Mechanical Performance"
DOI: 10.5284/1135462
title: Digital Archive from an Archaeological Evaluation at Lower Wyke Farm, Andover, Hampshire, March 2024

description: This collection consists of site images and GIS data from an archaeological evaluation at Lower Wyke Farm, Andover, Hampshire. Works were conducted by Cotswold Archaeology in March 2024. A total of 6 trenches were excavated to test geophysical anomalies and characterise the results of the geophysical survey. A large, undated double ditched boundary feature was investigated in four trenches across the site. Possible extraction pits identified on the geophysics were proved to be natural hollows.
DOI: 10.15468/dl.zgm6ud
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Protomelas taeniolatus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025290-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yyg7pe
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia affinis (Baird & Girard, 1853)",
 "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 ((25.5395 -23.2724,25.1306 -24.0715,25.5395 -24.0715,25.5395 -23.2724))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022405-250525065834625/datasets/export for details.
DOI: 10.15468/dl.fq5f5d
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Werauhia macrochlamys (Mez & Wercklé) J.F.Morales"
 ]
}

 The dataset includes 40 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022404-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jrwpzq
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Racinaea hamaleana (É.Morren) Barfuss & W.Till"
 ]
}

 The dataset includes 113 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022117-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.5729505
title: Poetry and Elegant Prose [IO Bijapur 124]

description: Poetry and Elegant Prose.

This manuscript is now IO Bijapur 124 in the India Office collections.

[metadata: Otto Loth, A Catalogue of the Arabic Manuscripts in the Library of the India Office, (volume 1), no. 827 here with further notations and hyperlinks].


827.

B 124. Size 8 in. by 53/4 in.; foll. 186. Eleven and twelve lines in a page.

كتاب ديوان سيّدنا الشيخ الاجل .... وجيه الدين و بركة المسلمين عبدالرحيم بن احمد البرعى المهاجرى

A Collection of Ḳaṣîdahs of ‘ABD AL-RAḤÎM B. AḤMAD BUR’Î.

Begins: هذه القصائد من جملة ما وجد من شعر الشيخ الخ.

This collection contains ----

1.(foll. 8-27) poems addressed to God (الالهيّات) the first of which commences:

تجلت لوحدانية الحق انوارُ

2.(foll. 27-127) poems in praise of Muḥammad (النبويّات) ; 1

3.(foll. 127-186) poem on several Ṣûfîs (الصوفيّات) . Well written in a large hand. The collation with the original copy was finished on Saturday, the last of Rajab, 1038.

Prefixed are (foll. 1-7) two anonymous poems of a very ingenious design. The first of them begins:

لا تياسن فالرجا كم فرجا

The other, which is inscribed قصيدة مخلعة , commences:

ملك سما ذو اكمال زانه كرم

It consists of twenty verses. All of these, as well as single sections of them, which are written in red, may be transposed, and the poem may thereby be varied in 360, or, as is added in a postscript, rather in millions of ways.

Cat. 223, xi.

 

 

1 A poem of this kind is to be found in Cat. Bodl. i. 254, no. MCCXXVI. 2; cf. ibid. ii. 614.
DOI: 10.5281/zenodo.5729504
title: Poetry and Elegant Prose [IO Bijapur 124]

description: Poetry and Elegant Prose.

This manuscript is now IO Bijapur 124 in the India Office collections.

[metadata: Otto Loth, A Catalogue of the Arabic Manuscripts in the Library of the India Office, (volume 1), no. 827 here with further notations and hyperlinks].


827.

B 124. Size 8 in. by 53/4 in.; foll. 186. Eleven and twelve lines in a page.

كتاب ديوان سيّدنا الشيخ الاجل .... وجيه الدين و بركة المسلمين عبدالرحيم بن احمد البرعى المهاجرى

A Collection of Ḳaṣîdahs of ‘ABD AL-RAḤÎM B. AḤMAD BUR’Î.

Begins: هذه القصائد من جملة ما وجد من شعر الشيخ الخ.

This collection contains ----

1.(foll. 8-27) poems addressed to God (الالهيّات) the first of which commences:

تجلت لوحدانية الحق انوارُ

2.(foll. 27-127) poems in praise of Muḥammad (النبويّات) ; 1

3.(foll. 127-186) poem on several Ṣûfîs (الصوفيّات) . Well written in a large hand. The collation with the original copy was finished on Saturday, the last of Rajab, 1038.

Prefixed are (foll. 1-7) two anonymous poems of a very ingenious design. The first of them begins:

لا تياسن فالرجا كم فرجا

The other, which is inscribed قصيدة مخلعة , commences:

ملك سما ذو اكمال زانه كرم

It consists of twenty verses. All of these, as well as single sections of them, which are written in red, may be transposed, and the poem may thereby be varied in 360, or, as is added in a postscript, rather in millions of ways.

Cat. 223, xi.

 

 

1 A poem of this kind is to be found in Cat. Bodl. i. 254, no. MCCXXVI. 2; cf. ibid. ii. 614.
DOI: 10.15468/dl.vbketv
title: Occurrence Download

description: A dataset containing 1383949 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Ichneumonidae"
 ]
}

 The dataset includes 1383949 records from 1303 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022103-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9uhdyg
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Labeo umbratus (Smith, 1841)",
 "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 ((25.0214 -34.0501,25.5395 -34.1098,25.5395 -32.9007,20.509 -32.9007,20.509 -34.5676,20.524 -34.555,20.8859 -34.5419,20.9606 -34.4398,21.2995 -34.5131,21.5296 -34.4338,21.8696 -34.4439,22.0323 -34.2835,22.221 -34.2428,22.2566 -34.1304,22.5993 -34.0741,22.9652 -34.1674,23.4069 -34.1858,23.4955 -34.0792,23.6056 -34.0563,24.8471 -34.2877,24.9447 -34.2397,25.0214 -34.0501))"
 ]
}

 The dataset includes 130 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021964-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15597586
title: AI4InSync Reconstruction Tutorial

description: Data required to run the tutorial [data/RECONSTRUCTIONS_MAPS.nc] and [data/RECONSTRUCTION_MASK.nc] on https://github.com/lahoffman/AI4InSync 







In this tutorial we train a machine learning (ML) model to learn daily Arctic sea ice velocity from information about wind velocity, sea ice concentration, latitude, longitude, and day of year. The ML model will be trained using outputs from several CMIP6 models subsampled at locations of Ice Tethered Profiler (ITP) observations. The model is trained on data from 2005-2014. Reconstructions are based on the 2005-2010 period. The data included here is pre-processed and includes CMIP6 outputs subsampled at ITP locations,



 

We use zonal and meridional sea ice velocity (siu, siv), wind velocity (uas, vas), and sea ice concentration (siconc) from the historical runs of the following CMIP6 models and ensemble members:


1. CanESM5 [10]

2. IPSL-CM6A-LR [31]

3. MIROC6 [10]


The data from CMIP6 can be found on the Earth System Grid Federation (ESFF) nodes: https://esgf-node.llnl.gov/projects/cmip6/


Eyring, V., Bony, S., Meehl, G., Senior, C., Stevens, B., Ronald, S., & Taylor, K. (2015, 12). Overview of the coupled model intercomparison project phase 6 (cmip6) experimental design and organisation. Geoscientific Model Development Discussions, 8 , 10539-10583. doi: 10.5194/gmdd-8-10539-2015

 




TOOLE, JOHN M., et al. “THE ICE-TETHERED PROFILER: ARGO OF THE ARCTIC.” Oceanography, vol. 24, no. 3, 2011, pp. 126–35. JSTOR, http://www.jstor.org/stable/24861307.


Krishfield, R., Toole, J., Proshutinsky, A., & Timmermans, M. (2008). Automated Ice-Tethered Profilers for Seawater Observations under Pack Ice in All Seasons, Journal of Atmospheric and Oceanic Technology, 25(11), 2091-2105.
DOI: 10.5281/zenodo.15597587
title: AI4InSync Reconstruction Tutorial

description: Data required to run the tutorial [data/RECONSTRUCTIONS_MAPS.nc] and [data/RECONSTRUCTION_MASK.nc] on https://github.com/lahoffman/AI4InSync 







In this tutorial we train a machine learning (ML) model to learn daily Arctic sea ice velocity from information about wind velocity, sea ice concentration, latitude, longitude, and day of year. The ML model will be trained using outputs from several CMIP6 models subsampled at locations of Ice Tethered Profiler (ITP) observations. The model is trained on data from 2005-2014. Reconstructions are based on the 2005-2010 period. The data included here is pre-processed and includes CMIP6 outputs subsampled at ITP locations,



 

We use zonal and meridional sea ice velocity (siu, siv), wind velocity (uas, vas), and sea ice concentration (siconc) from the historical runs of the following CMIP6 models and ensemble members:


1. CanESM5 [10]

2. IPSL-CM6A-LR [31]

3. MIROC6 [10]


The data from CMIP6 can be found on the Earth System Grid Federation (ESFF) nodes: https://esgf-node.llnl.gov/projects/cmip6/


Eyring, V., Bony, S., Meehl, G., Senior, C., Stevens, B., Ronald, S., & Taylor, K. (2015, 12). Overview of the coupled model intercomparison project phase 6 (cmip6) experimental design and organisation. Geoscientific Model Development Discussions, 8 , 10539-10583. doi: 10.5194/gmdd-8-10539-2015

 




TOOLE, JOHN M., et al. “THE ICE-TETHERED PROFILER: ARGO OF THE ARCTIC.” Oceanography, vol. 24, no. 3, 2011, pp. 126–35. JSTOR, http://www.jstor.org/stable/24861307.


Krishfield, R., Toole, J., Proshutinsky, A., & Timmermans, M. (2008). Automated Ice-Tethered Profilers for Seawater Observations under Pack Ice in All Seasons, Journal of Atmospheric and Oceanic Technology, 25(11), 2091-2105.
DOI: 10.15468/dl.rd6p78
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is United States of America",
 "TaxonKey is Spergula arvensis L.",
 "Year 1840-1860"
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021522-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bykvwb
title: Occurrence Download

description: A dataset listing the 27 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.2 -0.1,-75.6 -0.1,-75.6 0.1,-76.2 0.1,-76.2 -0.1))",
 "HasCoordinate is true",
 "IucnRedListCategory is one of (EN, CR, VU, NT)",
 "OccurrenceStatus is Present",
 "Year 1996-2025"
 ]
}

 The dataset's 27 records were derived from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018981-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.