cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24205010
title: Revisiting the truncated lamin A produced by a commonly used strain of <i>Lmna</i> knockout mice

description: The <i>Lmna</i> knockout mouse (<i>Lmna</i><sup>–/–</sup>) created by Sullivan and coworkers in 1999 has been widely used to examine lamin A/C function. The knockout allele contains a deletion of <i>Lmna</i> intron 7–exon 11 sequences and was reported to be a null allele. Later, Jahn and coworkers discovered that the mutant allele produces a 54-kDa truncated lamin A and identified, by RT-PCR, a <i>Lmna</i> cDNA containing exon 1–7 + exon 12 sequences. Because exon 12 encodes prelamin A’s <i>CaaX</i> motif, the mutant lamin A is assumed to be farnesylated. In the current study, we found that the truncated lamin A in <i>Lmna</i><sup>–/–</sup> mouse embryonic fibroblasts (MEFs) was predominantly nucleoplasmic rather than at the nuclear rim, leading us to hypothesize that it was not farnesylated. Our study revealed that the most abundant <i>Lmna</i> transcripts in <i>Lmna</i><sup>–/–</sup> MEFs contain exon 1–7 but not exon 12 sequences. Exon 1–7 + exon 12 transcripts were detectable by PCR but in trace amounts. We suspect that these findings explain the nucleoplasmic distribution of the truncated lamin A in <i>Lmna</i><sup>–/–</sup> MEFs, and subsequent cell transduction experiments support this suspicion. A truncated lamin A containing exon 1–7 sequence was nucleoplasmic, whereas a lamin A containing exon 1–7 + exon 12 sequences was located along the nuclear rim. Our study explains the nucleoplasmic targeting of truncated lamin A in <i>Lmna</i><sup>–/–</sup> MEFs and adds to our understanding of a commonly used strain of <i>Lmna</i><sup>–/–</sup> mice.
DOI: 10.6084/m9.figshare.24205010.v1
title: Revisiting the truncated lamin A produced by a commonly used strain of <i>Lmna</i> knockout mice

description: The <i>Lmna</i> knockout mouse (<i>Lmna</i><sup>–/–</sup>) created by Sullivan and coworkers in 1999 has been widely used to examine lamin A/C function. The knockout allele contains a deletion of <i>Lmna</i> intron 7–exon 11 sequences and was reported to be a null allele. Later, Jahn and coworkers discovered that the mutant allele produces a 54-kDa truncated lamin A and identified, by RT-PCR, a <i>Lmna</i> cDNA containing exon 1–7 + exon 12 sequences. Because exon 12 encodes prelamin A’s <i>CaaX</i> motif, the mutant lamin A is assumed to be farnesylated. In the current study, we found that the truncated lamin A in <i>Lmna</i><sup>–/–</sup> mouse embryonic fibroblasts (MEFs) was predominantly nucleoplasmic rather than at the nuclear rim, leading us to hypothesize that it was not farnesylated. Our study revealed that the most abundant <i>Lmna</i> transcripts in <i>Lmna</i><sup>–/–</sup> MEFs contain exon 1–7 but not exon 12 sequences. Exon 1–7 + exon 12 transcripts were detectable by PCR but in trace amounts. We suspect that these findings explain the nucleoplasmic distribution of the truncated lamin A in <i>Lmna</i><sup>–/–</sup> MEFs, and subsequent cell transduction experiments support this suspicion. A truncated lamin A containing exon 1–7 sequence was nucleoplasmic, whereas a lamin A containing exon 1–7 + exon 12 sequences was located along the nuclear rim. Our study explains the nucleoplasmic targeting of truncated lamin A in <i>Lmna</i><sup>–/–</sup> MEFs and adds to our understanding of a commonly used strain of <i>Lmna</i><sup>–/–</sup> mice.
DOI: 10.6084/m9.figshare.22651997.v1
title: Lamin B1 overexpression alters chromatin organization and gene expression

description: Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.
DOI: 10.6084/m9.figshare.22224078
title: Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies

description: This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.
DOI: 10.6084/m9.figshare.22224078.v1
title: Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies

description: This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.
DOI: 10.17045/sthlmuni.24324886
title: Data set for the article "Refining Protein Amide I Spectrum Simulations with Simple yet Effective Electrostatic Models for Local Wavenumbers and Dipole Derivative Magnitudes" published by Baronio & Barth in Physical Chemistry Chemical Physics

description: Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures – α-helices, parallel and antiparallel β-sheets – with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the C=O bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment.
DOI: 10.17045/sthlmuni.24324886.v1
title: Data set for the article "Refining Protein Amide I Spectrum Simulations with Simple yet Effective Electrostatic Models for Local Wavenumbers and Dipole Derivative Magnitudes" published by Baronio & Barth in Physical Chemistry Chemical Physics

description: Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures – α-helices, parallel and antiparallel β-sheets – with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the C=O bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment.
DOI: 10.5281/zenodo.10401257
title: Minute-Level Human Activity and Particulate Matter Exposure Dataset from Ljubljana, Slovenia

description: This dataset encompasses detailed measurements of human activities and particulate matter exposure at a minute-level resolution, collected in Ljubljana, Slovenia from September 24 to October 31, 2020. Data was gathered from 18 participants using a combination of devices: a personal particulate matter monitor (PPM), a Garmin Vivosmart 3 smart activity tracker (SAT), and the Clockify app. The PPM provided real-time measurements of particulate matter concentrations (PM1, PM2.5, and PM10), as well as environmental parameters like temperature, humidity, and altitude. The SAT tracker offered insights into personal health data, including average heart rate and metabolic equivalent of task (MET). Clockify app was utilized for detailed logging of various activities categorized with minute accuracy.

Key variables included in the dataset are:



Participant ID

Date of data collection

Time of data recording (minute accuracy)

Specific task or activity performed

Particulate matter - PM1 - concentrations

Particulate matter - PM2.5 - concentrations

Particulate matter - PM10 - concentrations

Environmental temperature

Relative humidity

Altitude

Speed

Average heart rate

Metabolic equivalent of task


This dataset offers a resource for exploring the interplay between individual behaviors and air pollution exposure, with applications in environmental health research and the development of machine learning models for activity recognition.
DOI: 10.5281/zenodo.10401258
title: Minute-Level Human Activity and Particulate Matter Exposure Dataset from Ljubljana, Slovenia

description: This dataset encompasses detailed measurements of human activities and particulate matter exposure at a minute-level resolution, collected in Ljubljana, Slovenia from September 24 to October 31, 2020. Data was gathered from 18 participants using a combination of devices: a personal particulate matter monitor (PPM), a Garmin Vivosmart 3 smart activity tracker (SAT), and the Clockify app. The PPM provided real-time measurements of particulate matter concentrations (PM1, PM2.5, and PM10), as well as environmental parameters like temperature, humidity, and altitude. The SAT tracker offered insights into personal health data, including average heart rate and metabolic equivalent of task (MET). Clockify app was utilized for detailed logging of various activities categorized with minute accuracy.

Key variables included in the dataset are:



Participant ID

Date of data collection

Time of data recording (minute accuracy)

Specific task or activity performed

Particulate matter - PM1 - concentrations

Particulate matter - PM2.5 - concentrations

Particulate matter - PM10 - concentrations

Environmental temperature

Relative humidity

Altitude

Speed

Average heart rate

Metabolic equivalent of task


This dataset offers a resource for exploring the interplay between individual behaviors and air pollution exposure, with applications in environmental health research and the development of machine learning models for activity recognition.
DOI: 10.6084/m9.figshare.24849756
title: Raw sequencing data for four pgymy grasshoppers: Exothotettix guangxiensis, Formosatettix longwangshanensis, Euparatettix sinufemoralis, and Systolederus zhengi

description: The high-throughput sequencing yielded extensive datasets for four distinct orthopteran species, namely <i>Euparatettix sinufemoralis</i>, <i>Exothotettix guangxiensis</i>, <i>Formosatettix longwangshanensis</i>, and <i>Systolederus zhengi</i>. Each species was subjected to paired-end sequencing, generating forward (R1) and reverse (R2) reads that provide comprehensive coverage of the genomic regions of interest. For the <i>Euparatettix sinufemoralis</i> sample, we secured 13,949,796 sequences from each end, accumulating a total of 2,092,469,400 bases with an equivalent file size of 2,275,444 KB for both R1 and R2 files. Similarly, for the <i>Exothotettix guangxiensis</i> sample, each of the paired-end files comprised 27,553,041 sequences, totaling 4,132,956,150 bases and necessitating 4,494,357 KB of storage. In the case of <i>Formosatettix longwangshanensis</i>, the sequence count stood at 13,836,864 and the number of bases recorded was 2,075,529,600 for each R1 and R2, each file consuming 2,257,023 KB of digital storage. The largest dataset was produced for <i>Systolederus zhengi</i>, with each paired file embedding 39,910,533 sequences and cumulatively amounting to 5,986,579,950 bases, all occupying 6,510,067 KB of storage.
DOI: 10.6084/m9.figshare.24849756.v1
title: Raw sequencing data for four pgymy grasshoppers: Exothotettix guangxiensis, Formosatettix longwangshanensis, Euparatettix sinufemoralis, and Systolederus zhengi

description: The high-throughput sequencing yielded extensive datasets for four distinct orthopteran species, namely <i>Euparatettix sinufemoralis</i>, <i>Exothotettix guangxiensis</i>, <i>Formosatettix longwangshanensis</i>, and <i>Systolederus zhengi</i>. Each species was subjected to paired-end sequencing, generating forward (R1) and reverse (R2) reads that provide comprehensive coverage of the genomic regions of interest. For the <i>Euparatettix sinufemoralis</i> sample, we secured 13,949,796 sequences from each end, accumulating a total of 2,092,469,400 bases with an equivalent file size of 2,275,444 KB for both R1 and R2 files. Similarly, for the <i>Exothotettix guangxiensis</i> sample, each of the paired-end files comprised 27,553,041 sequences, totaling 4,132,956,150 bases and necessitating 4,494,357 KB of storage. In the case of <i>Formosatettix longwangshanensis</i>, the sequence count stood at 13,836,864 and the number of bases recorded was 2,075,529,600 for each R1 and R2, each file consuming 2,257,023 KB of digital storage. The largest dataset was produced for <i>Systolederus zhengi</i>, with each paired file embedding 39,910,533 sequences and cumulatively amounting to 5,986,579,950 bases, all occupying 6,510,067 KB of storage.
DOI: 10.18112/openneuro.ds004141.v1.0.5
title: Targeting Dynamic Facial Processing Mechanisms in Superior Temporal Sulcus Using fMRI Neurofeedback
DOI: 10.6084/m9.figshare.24452773.v1
title: Hainan_Historical_Areca_distribution_from_1987_to_2022

description: In order to produce the areca plam distribution , we used data fusion and combined deep learning with machine learning techniques to map the geographical spatial distribution of areca palms on Hainan Island, China’s largest plantation area, from 1987 to 2022.
DOI: 10.6084/m9.figshare.24827661
title: <b>Data </b><b>from </b><b>A meta-analysis of peatland microbial diversity and function responses to climate change</b>

description: Database on microbial responses to climate change in peatlands. This file contains the effect sizes (EF) calculated for microbial richness, diversity, abundance and functions, as well as their variance (EF_var_g) and p-value (EF-pvalue), along with metadata (coordinates, community type, function, etc). <br>
DOI: 10.5281/zenodo.10401155
title: Dataset related to article "Long COVID-19 Cardiac Complications Are Associated With Autoimmunity to Cardiac Self-Antigens Sufficient to Cause Cardiac Dysfunction"

description: No abstract available
DOI: 10.5281/zenodo.10401156
title: Dataset related to article "Long COVID-19 Cardiac Complications Are Associated With Autoimmunity to Cardiac Self-Antigens Sufficient to Cause Cardiac Dysfunction"

description: No abstract available
DOI: 10.6084/m9.figshare.23578053
title: Mantle-hosted ophiolitic chromitites from Colombia: implications for petrogenesis and geodynamic evolution

description: Chromitite bodies can be found within ophiolitic mantle sections in three locations in Colombia: Medellín, Planeta Rica, and La Guajira. These chromitites are typically massive pods that are often surrounded by lateritic soil in Medellín and Planeta Rica, or small discoidal bodies in La Guajira. Inclusions in chromite are preserved to varying degrees in the three localities: olivine and pargasite are partially preserved in Medellín and Planeta Rica, whereas inclusions in La Guajira chromitites are completely altered to chlorite. Compositionally, chromite from the chromitites is high-Al in Medellín (Cr#[Cr/(Cr+Al) atomic ratio] = 0.41–0.51) and Planeta Rica (Cr# = 0.49–0.57), and high-Cr in La Guajira (Cr# = 0.75–0.76), whereas TiO<sub>2</sub> contents are low in the three localities (0.12–0.43 wt%). Regarding trace elements composition, the chromitites are similar to others formed in supra-subduction zone settings; the chromite from the high-Al chromitites is similar to that in MORB/BABB, whereas chromite from the high-Cr chromitites has a strong boninitic affinity. Chromitites from Planeta Rica are richer in Ti, possibly due to the presence of nearby gabbroic bodies and impregnated peridotites. The alteration in chromite rims and silicate matrix is related to metamorphic processes. Bulk-rock platinum-group element (PGE) contents range from 30 to 487 ppb, and chondrite-normalized PGE patterns show the typical enrichment in IPGE relative to PPGE observed in most ophiolitic chromitites. The estimated melts in equilibrium with the different chromitites correspond to MORB-like melts for the Medellín and Planeta Rica chromitites and to boninites for La Guajira chromitites. However, the estimated TiO<sub>2</sub> content in the melt is too low for a typical MORB, indicating back-arc basin basalts and a back-arc setting for the formation of the Medellín and Planeta Rica chromitites during the Late Triassic and the Late Jurassic, respectively. La Guajira chromitites are interpreted to have formed in a fore-arc basin related to subduction-initiation during Cretaceous times.
DOI: 10.6084/m9.figshare.23578053.v1
title: Mantle-hosted ophiolitic chromitites from Colombia: implications for petrogenesis and geodynamic evolution

description: Chromitite bodies can be found within ophiolitic mantle sections in three locations in Colombia: Medellín, Planeta Rica, and La Guajira. These chromitites are typically massive pods that are often surrounded by lateritic soil in Medellín and Planeta Rica, or small discoidal bodies in La Guajira. Inclusions in chromite are preserved to varying degrees in the three localities: olivine and pargasite are partially preserved in Medellín and Planeta Rica, whereas inclusions in La Guajira chromitites are completely altered to chlorite. Compositionally, chromite from the chromitites is high-Al in Medellín (Cr#[Cr/(Cr+Al) atomic ratio] = 0.41–0.51) and Planeta Rica (Cr# = 0.49–0.57), and high-Cr in La Guajira (Cr# = 0.75–0.76), whereas TiO<sub>2</sub> contents are low in the three localities (0.12–0.43 wt%). Regarding trace elements composition, the chromitites are similar to others formed in supra-subduction zone settings; the chromite from the high-Al chromitites is similar to that in MORB/BABB, whereas chromite from the high-Cr chromitites has a strong boninitic affinity. Chromitites from Planeta Rica are richer in Ti, possibly due to the presence of nearby gabbroic bodies and impregnated peridotites. The alteration in chromite rims and silicate matrix is related to metamorphic processes. Bulk-rock platinum-group element (PGE) contents range from 30 to 487 ppb, and chondrite-normalized PGE patterns show the typical enrichment in IPGE relative to PPGE observed in most ophiolitic chromitites. The estimated melts in equilibrium with the different chromitites correspond to MORB-like melts for the Medellín and Planeta Rica chromitites and to boninites for La Guajira chromitites. However, the estimated TiO<sub>2</sub> content in the melt is too low for a typical MORB, indicating back-arc basin basalts and a back-arc setting for the formation of the Medellín and Planeta Rica chromitites during the Late Triassic and the Late Jurassic, respectively. La Guajira chromitites are interpreted to have formed in a fore-arc basin related to subduction-initiation during Cretaceous times.