cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22117456.v1
title: Carbon taxes and agriculture: the benefit of a multilateral agreement

description: Reducing greenhouse gas emissions from agriculture is crucial to reach global and regional climate targets. However, the efficiency of unilateral climate policies aimed at taxing emissions might be hampered by carbon leakage. One way to eliminate leakage is to implement a global carbon tax. In this article, we study the effects of a carbon tax in agriculture on GHG emissions by simulating five policy scenarios using the CAPRI model; (i) an EU tax, (ii) an EU tax complemented with a border carbon adjustment mechanism (BCA), (iii) a global tax, (iv) a global tax scaled by GDP per capita, and (v) a low global tax at 1/10 of the tax level in the other scenarios. For the global scenarios, we also analyse the impact on food consumption and nutrient intake. We find that a global tax of EUR 120 per ton CO<sub>2</sub>-eq could reduce global agricultural emissions by 19%, but also jeopardizes food security in some parts of the world. A global tax at 1/10 of that rate (EUR 12) achieves a 3.2% reduction. In contrast, a unilateral EU tax of EUR 120 per ton CO<sub>2</sub>-eq, accompanied with a BCA, reduces global agricultural emissions by only 0.15%. A unilateral carbon tax in the EU causes significant emission leakage. This result depends strongly on differences in emission intensities between regions and on consumer preferences.A EUR 12 global carbon tax achieves a considerably larger global emission reduction than a EUR 120 unilateral EU carbon tax accompanied with a border carbon adjustment.A global carbon tax differentiated by GDP per capita is less effective than a uniform global carbon tax, as producers with higher emission intensities tend to get lower tax rates. Other ways of taking equity into account should be sought when designing climate policies in the agricultural sector. A unilateral carbon tax in the EU causes significant emission leakage. This result depends strongly on differences in emission intensities between regions and on consumer preferences. A EUR 12 global carbon tax achieves a considerably larger global emission reduction than a EUR 120 unilateral EU carbon tax accompanied with a border carbon adjustment. A global carbon tax differentiated by GDP per capita is less effective than a uniform global carbon tax, as producers with higher emission intensities tend to get lower tax rates. Other ways of taking equity into account should be sought when designing climate policies in the agricultural sector.
DOI: 10.13140/rg.2.2.11654.75845
title: Author: Chinwendu Enechi Title: Genogram of Mr. Obiora Mmaduka (A non-fictional story)
DOI: 10.25403/upresearchdata.25242886
title: Project seeking to improve Tuberculosis (TB) diagnostic services at primary healthcare clinics in high Tuberculosis (TB) burden settings

description: The data set contains various types of data from different objectives of the project including maps that show the geographic accessibility of TB diagnostic services at primary healthcare clinics, the raw data used to conduct an interrupted times series analysis that determined the impact of COVID-19 on TB diagnostic services, data used to determine the quality of TB diagnostic services at primary healthcare clinics assessed through an audit and the results from a nominal group technique that sought to find a means of improving TB diagnostic services for COVID-19 and related health emergencies.
DOI: 10.6084/m9.figshare.25053986.v1
title: "<b>Dam-calf contact rearing in Switzerland: Aspects of management and milking" - Supplemental material</b>

description: These tables present the supplements 1 and 2 to our manuscript "Dam-calf contact rearing in Switzerland: Aspects of management and milking". In includes results from the first part on our study on milkability in dam-calf contact systems in Switzerland. Supplement 1 shows the perceptions of the own dam-calf contact (DCC) system of the 17 interviewed DCC farmers. Supplement 2 demonstrates additional information given by the 1 farmers during the interview on weaning and milking.
DOI: 10.5522/04/25211312
title: Transcripts of interviews with pregnant women, their husbands, their mothers-in-law, health workers and decision-makers on antenatal screening for HIV, syphilis and hepatitis B in Nepal.

description: This study investigated the knowledge, attitude, and perceptions of pregnant women, their family members, healthcare workers and decision-makers on integrated antenatal screening. On the demand side, we conducted 26 semi-structured in-depth interviews with pregnant women, their husbands, and mothers-in-law in Kapilvastu and Kathmandu. On the supply side, we conducted 11 interviews with health workers involved in antenatal screening and local and national health system decision-makers.
DOI: 10.5522/04/25211312.v1
title: Transcripts of interviews with pregnant women, their husbands, their mothers-in-law, health workers and decision-makers on antenatal screening for HIV, syphilis and hepatitis B in Nepal.

description: This study investigated the knowledge, attitude, and perceptions of pregnant women, their family members, healthcare workers and decision-makers on integrated antenatal screening. On the demand side, we conducted 26 semi-structured in-depth interviews with pregnant women, their husbands, and mothers-in-law in Kapilvastu and Kathmandu. On the supply side, we conducted 11 interviews with health workers involved in antenatal screening and local and national health system decision-makers.
DOI: 10.6084/m9.figshare.19565871
title: Additional file 1 of Functional R2R3-MYB transcription factor NsMYB1, regulating anthocyanin biosynthesis, was relative to the fruit color differentiation in Nitraria sibirica Pall.

description: Additional file 1.
DOI: 10.6084/m9.figshare.19565871.v1
title: Additional file 1 of Functional R2R3-MYB transcription factor NsMYB1, regulating anthocyanin biosynthesis, was relative to the fruit color differentiation in Nitraria sibirica Pall.

description: Additional file 1.
DOI: 10.13140/rg.2.2.25076.53125
title: DESTROYING MORE TANKS OR MORE KILLED WAS NO CRITERIA - BUT ONLY LUCK AND WHO DECIDED THE MATTER ? 4 FF , 22 BALUCH AND 34 PUNJAB R AND S COMPARED
DOI: 10.13140/rg.2.2.18365.64481
title: DESTROYING MORE TANKS OR MORE KILLED WAS NO CRITERIA - BUT ONLY LUCK AND WHO DECIDED THE MATTER ? 4 FF , 22 BALUCH AND 34 PUNJAB R AND S COMPARED
DOI: 10.17031/rv13lu
title: 2014 Heiser, S. et al Plymouth Sound Undaria pinnatifida Records

description: This dataset contains records from Heiser et al (2014) Assessing the extent of establishment of Undaria pinnatifida in Plymouth Sound Special Area of Conservation, UK Marine Biodiversity Records, page 1 of 8 doi:10.1017/S1755267214000608; Vol. 7; e93. The first UK record of Undaria pinnatifida was in the Hamble estuary (1994) and it was found off Plymouth in 2003. The authors assessed the distribution of U. pinnatifida and native kelps and their allies in Plymouth Sound (at 0 to +1 m relative to Chart Datum). Undaria pinnatifida was widespread along rocky shores, on other hard substrata and grew in the same areas as Saccharina latissima and Saccorhiza polyschides. Undaria pinnatifida was significantly more abundant on vertical substrata than on upward-facing hard substrata. It was almost as common as all of the other kelp species combined on vertical substrata but was outnumbered by native species on upward-facing substrata. Undaria pinnatifida has become the visually dominant macroalga in marinas and has spread to surrounding natural habitats in Plymouth Sound. The extent to which it will out-compete native kelps requires monitoring, especially in conservation areas.
DOI: 10.13140/rg.2.2.15010.20160
title: DESTROYING MORE TANKS OR MORE KILLED WAS NO CRITERIA - BUT ONLY LUCK AND WHO DECIDED THE MATTER ? 4 FF , 22 BALUCH AND 34 PUNJAB R AND S COMPARED
DOI: 10.6084/m9.figshare.24917685
title: p20 and p30 clonesets

description: CTL repertoires from the paper "<b>High clonality and convergence of T cell response is a hallmark of effective peptide vaccine against B16 melanoma</b>"
DOI: 10.6084/m9.figshare.24917685.v1
title: p20 and p30 clonesets

description: CTL repertoires from the paper "<b>High clonality and convergence of T cell response is a hallmark of effective peptide vaccine against B16 melanoma</b>"
DOI: 10.5517/ccdc.csd.cc2d1q6d
title: CCDC 2206183: Experimental Crystal Structure Determination

description: Related Article: Hiroki Tanikubo, Takumi Matsuo, Shotaro Hayashi|2024|J.Cryst.Growth|631|127595|doi:10.1016/j.jcrysgro.2024.127595
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.21370615
title: Age and geochemistry of the Naxiguole banded iron formation (BIF), NW China: recurrence of superior-type BIF in the Neoproterozoic

description: The Naxiguole Banded Iron Formation (BIF), located in the Eastern Kunlun Orogenic Belt, Northwest China, is hosted by the Jinshuikou Group and has a Fe of 75 Mt at a grade of 15–28.83 wt.% Fe. In this paper, we use integrated petrological, geochemical, and geochronological data to limit the age and origin of the Naxiguole BIF. Country rocks mainly comprise marble, felsic paragneiss, plagioclase amphibolite schist, and biotite plagioclase gneiss. The features of sedimentary structure (blastopsammitic texture and blastobedding structure) and trace elements (e.g. La, Ni, Zr) from the country rock indicate that their protoliths are sedimentary rock. The 141 detrital zircons from the Jinshuikou Group yield a minimum age of 908 Ma, which can be considered the upper limit for the Naxiguole BIF. According to the age (602 Ma) of the mafic rocks intruding into the Jinshuikou Group, it is reasonable to assume that the formation age of BIF can be limited at 908–602 Ma (i.e. Neoproterozoic). The high contents of Al<sub>2</sub>O<sub>3</sub> + TiO<sub>2</sub> (3–6 wt.%), ΣREE (36–135 ppm) for BIF samples suggest that terrestrial clastic material contributed to BIF formation. The BIF samples show seawater-like features, such as depletion in LREEs, positive Y anomaly and high Y/Ho ratios (30.7–57.5, average = 42.5), implying that the Naxiguole BIF precipitated from seawater. The positive Eu/Eu*<sub>PAAS</sub> anomalies (average 1.52) suggest the influence of high-T hydrothermal fluids. Based on positive Eu anomalies and high terrestrial clastic components and no obvious Ce anomalies, the Naxiguole BIF was formed in an anoxic or suboxic sedimentary basin within active continental island arc, and is similar to Superior-type BIFs worldwide.
DOI: 10.6084/m9.figshare.21370615.v1
title: Age and geochemistry of the Naxiguole banded iron formation (BIF), NW China: recurrence of superior-type BIF in the Neoproterozoic

description: The Naxiguole Banded Iron Formation (BIF), located in the Eastern Kunlun Orogenic Belt, Northwest China, is hosted by the Jinshuikou Group and has a Fe of 75 Mt at a grade of 15–28.83 wt.% Fe. In this paper, we use integrated petrological, geochemical, and geochronological data to limit the age and origin of the Naxiguole BIF. Country rocks mainly comprise marble, felsic paragneiss, plagioclase amphibolite schist, and biotite plagioclase gneiss. The features of sedimentary structure (blastopsammitic texture and blastobedding structure) and trace elements (e.g. La, Ni, Zr) from the country rock indicate that their protoliths are sedimentary rock. The 141 detrital zircons from the Jinshuikou Group yield a minimum age of 908 Ma, which can be considered the upper limit for the Naxiguole BIF. According to the age (602 Ma) of the mafic rocks intruding into the Jinshuikou Group, it is reasonable to assume that the formation age of BIF can be limited at 908–602 Ma (i.e. Neoproterozoic). The high contents of Al<sub>2</sub>O<sub>3</sub> + TiO<sub>2</sub> (3–6 wt.%), ΣREE (36–135 ppm) for BIF samples suggest that terrestrial clastic material contributed to BIF formation. The BIF samples show seawater-like features, such as depletion in LREEs, positive Y anomaly and high Y/Ho ratios (30.7–57.5, average = 42.5), implying that the Naxiguole BIF precipitated from seawater. The positive Eu/Eu*<sub>PAAS</sub> anomalies (average 1.52) suggest the influence of high-T hydrothermal fluids. Based on positive Eu anomalies and high terrestrial clastic components and no obvious Ce anomalies, the Naxiguole BIF was formed in an anoxic or suboxic sedimentary basin within active continental island arc, and is similar to Superior-type BIFs worldwide.
DOI: 10.6084/m9.figshare.24516343
title: Mitochondrial subtype <i>MB-G3</i> contains potential novel biomarkers and therapeutic targets associated with prognosis of medulloblastoma

description: Medulloblastoma is the most common malignant brain tumor in children. There are four groups, each with different causal mutations, affected pathways and prognosis. Here, we investigated the role of mitochondria in medulloblastoma and whether there are differences between the different groups. We compared the gene expression levels in the four different medulloblastoma groups (MB-WNT, MB-SHH, MB-G3 and MB-G4), with the focus on genes associated with mitochondria. We used several tools including Salmon, Tximeta, DESeq2, BiomaRt, STRING, Ggplot2, EnhancedVolcano, Venny 2.1 and Metscape. A total of 668 genes were differentially expressed and the most abundant genes were associated with cell division pathway followed by modulation of chemical synaptic transmission. We also identified several genes (<i>ABAT</i>, <i>SOX9</i>, <i>ALDH5A</i>, <i>FOXM1</i>, <i>ABL1</i>, <i>NHLH1</i>, <i>NEUROD1</i> and <i>NEUROD2</i>) known to play vital role in medulloblastoma. Comparative expression analysis revealed OXPHOS complex-associated proteins of mitochondria. The most significantly expressed genes in the MB-SHH and MB-G4 groups were <i>AHCYL1</i> and <i>SFXN5</i> while <i>PAICS</i> was significantly upregulated in MB-WNT group. Notably, MB-G3 contained the most downregulated genes from the OXPHOS complexes, except <i>COX6B2</i> which was strongly upregulated. We show the importance of mitochondria and compare their role in the four different medulloblastoma groups.
DOI: 10.6084/m9.figshare.24516343.v1
title: Mitochondrial subtype <i>MB-G3</i> contains potential novel biomarkers and therapeutic targets associated with prognosis of medulloblastoma

description: Medulloblastoma is the most common malignant brain tumor in children. There are four groups, each with different causal mutations, affected pathways and prognosis. Here, we investigated the role of mitochondria in medulloblastoma and whether there are differences between the different groups. We compared the gene expression levels in the four different medulloblastoma groups (MB-WNT, MB-SHH, MB-G3 and MB-G4), with the focus on genes associated with mitochondria. We used several tools including Salmon, Tximeta, DESeq2, BiomaRt, STRING, Ggplot2, EnhancedVolcano, Venny 2.1 and Metscape. A total of 668 genes were differentially expressed and the most abundant genes were associated with cell division pathway followed by modulation of chemical synaptic transmission. We also identified several genes (<i>ABAT</i>, <i>SOX9</i>, <i>ALDH5A</i>, <i>FOXM1</i>, <i>ABL1</i>, <i>NHLH1</i>, <i>NEUROD1</i> and <i>NEUROD2</i>) known to play vital role in medulloblastoma. Comparative expression analysis revealed OXPHOS complex-associated proteins of mitochondria. The most significantly expressed genes in the MB-SHH and MB-G4 groups were <i>AHCYL1</i> and <i>SFXN5</i> while <i>PAICS</i> was significantly upregulated in MB-WNT group. Notably, MB-G3 contained the most downregulated genes from the OXPHOS complexes, except <i>COX6B2</i> which was strongly upregulated. We show the importance of mitochondria and compare their role in the four different medulloblastoma groups.
DOI: 10.5517/ccdc.csd.cc2f0tx6
title: CCDC 2235128: Experimental Crystal Structure Determination

description: Related Article: Clara Parella, Andreu Blanquer, Sohini Sinha, Evelyn Hümpfner, Jordi Hernando, Eloi Mora, Xavier Fontrodona, Zsolt Kelemen, Carme Nogués, Rosario Núñez, Isabel Romero|2024|Dyes Pigm.|224|111985|doi:10.1016/j.dyepig.2024.111985
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.12982031
title: Metadata record for the manuscript: Molecular landscape and efficacy of HER2-targeted therapy in patients with HER2-mutated metastatic breast cancer

description: <b>Summary</b>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Molecular landscape and efficacy of HER2-targeted therapy
in patients with HER2-mutated metastatic breast cancer”.

The
related study investigated the effect of HER2 mutations on the likelihood of a
response to HER2-targeted therapies in patients stratified according to their
HER2 amplification status, under the hypothesis that this might help clinicians
choose more precise HER2-targeted therapies.<br>

 

<b>Data
access</b>

The
genome sequence data have been deposited in China National GeneBank DataBase (CNGBdb): https://db.cngb.org/search/project/CNP0001305/. The file “Supplementary Data 1.xlsx” lists somatic mutations identified in 1184 patients, and is
available together with this metadata record. The files “Clinical
data20200728.xlsx” and “Patient therapy responses and adverse events data.xlsx”
contain data on the patients—these datasets are not publicly available in order
to protect patient privacy, and dataset requests should be sent to Dr Ma; contact details below:<br>

Dr
Fei Ma<br>National
Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital，Chinese
Academy of Medical Sciences and Peking Union Medical College<br>Medical Oncology<br>No. 17 Panjiayuan Nanli, Beijing, 100021, China<br>Beijing, 100021<br>China<br>8610-87788060<br>drmafei@126.com

<br>
<b>Name of Institutional Review Board or
ethics committee that approved the study<br></b>Regulatory and Ethics Committees of National Cancer
Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of
Medical Sciences and Peking Union Medical College (ref: 16-038/1117 and
17-180/1436).

<b>Clinical trial registry URL<br></b>https://clinicaltrials.gov/ct2/show/NCT03412383?cond=NCT03412383&draw=2&rank=1
DOI: 10.6084/m9.figshare.12982031.v1
title: Metadata record for the manuscript: Molecular landscape and efficacy of HER2-targeted therapy in patients with HER2-mutated metastatic breast cancer

description: <b>Summary</b>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Molecular landscape and efficacy of HER2-targeted therapy
in patients with HER2-mutated metastatic breast cancer”.

The
related study investigated the effect of HER2 mutations on the likelihood of a
response to HER2-targeted therapies in patients stratified according to their
HER2 amplification status, under the hypothesis that this might help clinicians
choose more precise HER2-targeted therapies.<br>

 

<b>Data
access</b>

The
genome sequence data have been deposited in China National GeneBank DataBase (CNGBdb): https://db.cngb.org/search/project/CNP0001305/. The file “Supplementary Data 1.xlsx” lists somatic mutations identified in 1184 patients, and is
available together with this metadata record. The files “Clinical
data20200728.xlsx” and “Patient therapy responses and adverse events data.xlsx”
contain data on the patients—these datasets are not publicly available in order
to protect patient privacy, and dataset requests should be sent to Dr Ma; contact details below:<br>

Dr
Fei Ma<br>National
Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital，Chinese
Academy of Medical Sciences and Peking Union Medical College<br>Medical Oncology<br>No. 17 Panjiayuan Nanli, Beijing, 100021, China<br>Beijing, 100021<br>China<br>8610-87788060<br>drmafei@126.com

<br>
<b>Name of Institutional Review Board or
ethics committee that approved the study<br></b>Regulatory and Ethics Committees of National Cancer
Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of
Medical Sciences and Peking Union Medical College (ref: 16-038/1117 and
17-180/1436).

<b>Clinical trial registry URL<br></b>https://clinicaltrials.gov/ct2/show/NCT03412383?cond=NCT03412383&draw=2&rank=1
DOI: 10.14473/csda/icjgda/iffaq2
title: kf_data_bez_diakritiky_w4_chps_cz_v1.0_ENG.tab

description: Data_Contact forms
DOI: 10.6084/m9.figshare.14555040
title: The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome

description: Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) <i>in vivo</i> and <i>in vitro</i>. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of <i>Lsh</i> leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus <i>Lsh</i> knock-out MEFs and ESCs showed that in absence of <i>Lsh</i>, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon <i>Lsh</i> knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
DOI: 10.6084/m9.figshare.14555040.v1
title: The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome

description: Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) <i>in vivo</i> and <i>in vitro</i>. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of <i>Lsh</i> leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus <i>Lsh</i> knock-out MEFs and ESCs showed that in absence of <i>Lsh</i>, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon <i>Lsh</i> knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.