cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24159505.v1
title: Additional file 2 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host

description: Additional file 2. Supplemental Table 4. Sequencing statistics for all samples split by Group.
DOI: 10.22008/fk2/kule1q/1tjhz6
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_04_29.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_04_29.nc, date: 2023-04-29
DOI: 10.22008/fk2/kule1q/rrbybt
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_04_30.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_04_30.nc, date: 2023-04-30
DOI: 10.22008/fk2/qkvxc9/h3azwq
title: SICEv2.3.2_Svalbard_1000m_2023_08_30.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_08_30.nc, date: 2023-08-30
DOI: 10.5281/zenodo.7405286
title: Dataset: Inter-Row Management and Clay Content Influence Acari and Collembola Abundances in Vineyards

description: Data repository of the raw data for the data analysis of the article: "Inter-Row Management and Clay Content Influence Acari and Collembola Abundances in Vineyards" published in Horticulturae
DOI: 10.5281/zenodo.7405287
title: Dataset: Inter-Row Management and Clay Content Influence Acari and Collembola Abundances in Vineyards

description: Data repository of the raw data for the data analysis of the article: "Inter-Row Management and Clay Content Influence Acari and Collembola Abundances in Vineyards" published in Horticulturae
DOI: 10.22008/fk2/kule1q/4pisfg
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_01.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_01.nc, date: 2023-05-01
DOI: 10.22008/fk2/qkvxc9/vvacur
title: SICEv2.3.2_Svalbard_1000m_2023_08_31.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_08_31.nc, date: 2023-08-31
DOI: 10.22008/fk2/qkvxc9/xjqsj8
title: SICEv2.3.2_Svalbard_1000m_2023_09_01.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_09_01.nc, date: 2023-09-01
DOI: 10.22008/fk2/kule1q/l9i7kl
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_02.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_02.nc, date: 2023-05-02
DOI: 10.22008/fk2/qkvxc9/zi9ako
title: SICEv2.3.2_Svalbard_1000m_2023_09_02.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_09_02.nc, date: 2023-09-02
DOI: 10.22008/fk2/kule1q/r9qkso
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_03.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_03.nc, date: 2023-05-03
DOI: 10.22008/fk2/qkvxc9/v3gdl9
title: SICEv2.3.2_Svalbard_1000m_2023_09_03.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_09_03.nc, date: 2023-09-03
DOI: 10.22008/fk2/kule1q/frygqn
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_05.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_05.nc, date: 2023-05-05
DOI: 10.22008/fk2/qkvxc9/lde55f
title: SICEv2.3.2_Svalbard_1000m_2023_09_04.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_09_04.nc, date: 2023-09-04
DOI: 10.22008/fk2/kule1q/p93905
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_06.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_06.nc, date: 2023-05-06
DOI: 10.22008/fk2/kule1q/xgaric
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_07.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_07.nc, date: 2023-05-07
DOI: 10.22008/fk2/qkvxc9/bxlpsd
title: SICEv2.3.2_Svalbard_1000m_2023_09_05.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_09_05.nc, date: 2023-09-05
DOI: 10.6084/m9.figshare.23949825
title: Additional file 2 of Epigenetic instability caused by absence of CIZ1 drives transformation during quiescence cycles

description: Additional file 2: SDataset 1. Excel file showing mean data with significance indicators for all transcription units that are changed upon entry to quiescence in WT PEFs. Sheet 1, effect of serum withdrawal. Sheet 2, effect of contact inhibition. Sheet 3, core murine quiescence genes. Sheet 5 and 6, GSEA output for up and down regulated genes respectively, showing significance indicators for GO terms used to create the graph shown in Fig 2.
DOI: 10.6084/m9.figshare.24124016
title: Additional file 3 of The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees

description: Additional file 3. Data S2. A Raw text file containing the gene symbol of each gene with cell-type-restricted differential expression. One gene is listed per line.
DOI: 10.22008/fk2/kule1q/k3jpqf
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_08.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_08.nc, date: 2023-05-08
DOI: 10.22008/fk2/qkvxc9/ncvyqa
title: SICEv2.3.2_Svalbard_1000m_2023_09_06.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_09_06.nc, date: 2023-09-06
DOI: 10.22008/fk2/kule1q/le8ky8
title: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_09.nc

description: SICEv2.3.2 output: SICEv2.3.2_SouthernArcticCanada_1000m_2023_05_09.nc, date: 2023-05-09
DOI: 10.22008/fk2/qkvxc9/kfitgh
title: SICEv2.3.2_Svalbard_1000m_2023_09_07.nc

description: SICEv2.3.2 output: SICEv2.3.2_Svalbard_1000m_2023_09_07.nc, date: 2023-09-07
DOI: 10.6084/m9.figshare.24144129.v1
title: Additional file 3 of Amyloid fibril proteomics of AD brains reveals modifiers of aggregation and toxicity

description: Additional file 3: Table S1. Summary of the human subject brains. Overall, 1 control human brain tissues were used; age, gender, race and other relevant information is provided in sheet 1. For AD human samples, we obtained 13 and 23 human brain tissues with amyloid scores 2 and 3, respectively. All the relevant information are provided for each human sample, including their gender, age, race, postmortem time (PMT), clinical Braak stage, CERAD scores, etc.
DOI: 10.6084/m9.figshare.7996805.v1
title: Additional file 1: of Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies

description: Table S1. Reactions modified to curate the Plasmodium falciparum genome-scale metabolic model. (ST2A and ST2B) Table S2. Down-regulated Differentially Expressed Genes in (A) Short and (B) Long-term Chloroquine-treated Parasites. The gene IDs, corresponding gene names, and fold changes of significantly down-regulated genes in response to chloroquine treatment. Table S3. Up-regulated Differentially Expressed Genes in (A) Short and (B) Long-term Chloroquine-treated Parasites. The gene IDs, corresponding gene names, and fold changes of significantly up-regulated genes in response to chloroquine treatment. Table S4. Significant Down Regulation of Metabolic Genes Arising from Chloroquine Treatment. A: Metabolic DEGs Common to Long and Short-term Treated Conditions. B: Metabolic DEGs Unique to Short-term Treated Condition. The gene IDs, corresponding gene names, and metabolic subsystems of genes with significant expression changes in response to chloroquine treatment. C: Metabolic DEGs Unique to Long-term Treated Condition. The gene IDs, corresponding gene names, and metabolic subsystems of genes with significant expression changes in response to chloroquine treatment. Table S5. Reactions Essential in only Chloroquine-Treated Models. The reaction IDs, corresponding enzyme names, reaction formulas, and metabolic subsystems of essential reactions common to chloroquine-treated condition models constructed with varying growth thresholds (30–80%). Table S6. Reactions Essential in only the Short-Term Treatment Condition. Table S7. Reactions Essential in only the Long-Term Treatment Condition. Table S8. Flux Values for Isoprenoid Metabolism Reactions. Results represent median flux values across condition models constructed with varying growth thresholds (30–80%). Bolded reactions are represented in Fig. 4. Table S9. Flux Values for Folate Metabolism Reactions. Results represent median flux values across condition models constructed with varying growth thresholds (30–80%). Bolded reactions are represented in Fig. 5. (ODS 28 kb)
DOI: 10.6084/m9.figshare.7996598
title: Toxicity percentage at different concentrations of hydro-alcoholic extract

description: Toxicity percentage at different concentrations of hydro-alcoholic extract. Note: phytochemical analyses based on the color change (please see three replications)
DOI: 10.6084/m9.figshare.7996577
title: Appendix_Item_Level_Descriptives .pdf

description: Appendix file -- descriptive statistic<br>
DOI: 10.6084/m9.figshare.7996577.v1
title: Appendix_Item_Level_Descriptives .pdf

description: Appendix file -- descriptive statistic<br>
DOI: 10.6084/m9.figshare.7996598.v1
title: Toxicity percentage at different concentrations of hydro-alcoholic extract

description: Toxicity percentage at different concentrations of hydro-alcoholic extract
DOI: 10.6084/m9.figshare.7996436
title: LEARNING STYLES PREFERENCE, GENDER AND ENGLISH LANGUAGE PERFORMANCE OF EFL LIBYAN SECONDARY SCHOOL STUDENTS IN MALAYSIA

description: The purpose of this study is to determine if there were relationships among learning style preference, gender and English language performance of EFL Libyan secondary school students in Malaysia. Specifically, the study was guided by three research questions focused on Libyan student’s level of performance in EFL class in Malaysia, their learning styles and gender, and the relationship between students’ learning styles and their English language performance. There has been a limited number of studies on Libyan secondary schools’ student studying in Malaysia. This study was a correlational study involving 108 Libyan secondary school students in Malaysia. Data was analysed using the statistical package for Social Science (SPSS, version 20.0). The results showed that most learners who participated in this study had a medium proficiency level in the English language and majority of the Libyan students preferred independent learning style. It was found that there was a difference in the learning styles preferred by female and male secondary school students. The study also revealed that there was no significant relationship between students’ overall learning styles and their English language performance and. Recommendations were offered. Future researches could use more than one school to obtain accurate results and could also focus on gender bias
DOI: 10.6084/m9.figshare.7996439
title: Individual-based expression for 87 candidate genes after six days of treatment

description: The gene expression values provided are normalized and then log transformed as described in the main text.
DOI: 10.6084/m9.figshare.7996430
title: 立山周辺の湖沼水，温泉水，河川水，池塘の水質分析結果（2018）

description: 室堂平周辺の湖沼は、地獄谷に隣接しており、その水質は、噴気孔との位置関係によって異なっていた。特に、リンドウ池は影響が大きかった (表1)。 地獄谷内の紺屋川は温泉の影響を受け、pHの値は1.94～2.62、硫酸イオン濃度は125.3～620.4 mg/L、塩化物イオン濃度は63.3～404.8 mg/Lであった。立山カルデラ内の新湯は、pHが3.39と高めであるが、硫酸イオン濃度、塩化物イオン濃度は，それぞれ，293.2mg/L，149.7mg/Lと高く、pHが高い理由は中和成分のナトリウムイオン濃度が高いためである(表2)。 黒部川源流域の水では、降水起源と考えられる水と、地下水起源と考えられる水の両方が見られた。一方、餓鬼の田圃の水はpHが低く、カルシウムイオン濃度も低いことから、降水がそのままたまったものと考えられた(表3)。 奥大日岳稜線の池沼の水質は降水の水質と同等であった(表4)。 立山の追分地内の湿原に点在する池塘の水質は、調査したすべての池塘で降水の水質と同等で、蒸発による濃縮もみられた(表5)。
DOI: 10.6084/m9.figshare.7996439.v1
title: Individual-based expression for 87 candidate genes after six days of treatment

description: The gene expression values provided are normalized and then log transformed as described in the main text.
DOI: 10.6084/m9.figshare.7996430.v1
title: 立山周辺の湖沼水，温泉水，河川水，池塘の水質分析結果（2018）

description: 室堂平周辺の湖沼は、地獄谷に隣接しており、その水質は、噴気孔との位置関係によって異なっていた。特に、リンドウ池は影響が大きかった (表1)。 地獄谷内の紺屋川は温泉の影響を受け、pHの値は1.94～2.62、硫酸イオン濃度は125.3～620.4 mg/L、塩化物イオン濃度は63.3～404.8 mg/Lであった。立山カルデラ内の新湯は、pHが3.39と高めであるが、硫酸イオン濃度、塩化物イオン濃度は，それぞれ，293.2mg/L，149.7mg/Lと高く、pHが高い理由は中和成分のナトリウムイオン濃度が高いためである(表2)。 黒部川源流域の水では、降水起源と考えられる水と、地下水起源と考えられる水の両方が見られた。一方、餓鬼の田圃の水はpHが低く、カルシウムイオン濃度も低いことから、降水がそのままたまったものと考えられた(表3)。 奥大日岳稜線の池沼の水質は降水の水質と同等であった(表4)。 立山の追分地内の湿原に点在する池塘の水質は、調査したすべての池塘で降水の水質と同等で、蒸発による濃縮もみられた(表5)。
DOI: 10.6084/m9.figshare.7996397
title: Global analysis of chaperone effects using a reconstituted cell-free translation system

description: Protein folding is often hampered by protein aggregation, which can be prevented by a variety of chaperones in the cell. A dataset that evaluates which chaperones are effective for aggregation-prone proteins would provide an invaluable resource not only for understanding the roles of chaperones, but also for broader applications in protein science and engineering. Therefore, we comprehensively evaluated the effects of the major Escherichia coli chaperones, trigger factor, DnaK/DnaJ/GrpE, and GroEL/GroES, on ∼800 aggregation-prone cytosolic E. coli proteins, using a reconstituted chaperone-free translation system. Statistical analyses revealed the robustness and the intriguing properties of chaperones. The DnaK and GroEL systems drastically increased the solubilities of hundreds of proteins with weak biases, whereas trigger factor had only a marginal effect on solubility. The combined addition of the chaperones was effective for a subset of proteins that were not rescued by any single chaperone system, supporting the synergistic effect of these chaperones. The resource, which is accessible via a public database, can be used to investigate the properties of proteins of interest in terms of their solubilities and chaperone effects.
DOI: 10.6084/m9.figshare.7996403
title: Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding

description: A subset of the proteome is prone to aggregate formation, which is prevented by chaperones in the cell. To investigate whether the basic principle underlying the aggregation process is common in prokaryotes and eukaryotes, we conducted a large-scale aggregation analysis of ~500 cytosolic budding yeast proteins using a chaperone-free reconstituted translation system, and compared the obtained data with that of ~3,000 Escherichia coli proteins reported previously. Although the physicochemical properties affecting the aggregation propensity were generally similar in yeast and E. coli proteins, the susceptibility of aggregation in yeast proteins were positively correlated with the presence of intrinsically disordered regions (IDRs). Notably, the aggregation propensity was not significantly changed by a removal of IDRs in model IDR-containing proteins, suggesting that the properties of ordered regions in these proteins are the dominant factors for aggregate formation. We also found that the proteins with longer IDRs were disfavored by E. coli chaperonin GroEL/ES, whereas both bacterial and yeast Hsp70/40 chaperones have a strong aggregation-prevention effect even for proteins possessing IDRs. These results imply that a key determinant to discriminate the eukaryotic proteomes from the prokaryotic proteomes in terms of protein folding would be the attachment of IDRs.
DOI: 10.6084/m9.figshare.7996403.v1
title: Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding

description: A subset of the proteome is prone to aggregate formation, which is prevented by chaperones in the cell. To investigate whether the basic principle underlying the aggregation process is common in prokaryotes and eukaryotes, we conducted a large-scale aggregation analysis of ~500 cytosolic budding yeast proteins using a chaperone-free reconstituted translation system, and compared the obtained data with that of ~3,000 Escherichia coli proteins reported previously. Although the physicochemical properties affecting the aggregation propensity were generally similar in yeast and E. coli proteins, the susceptibility of aggregation in yeast proteins were positively correlated with the presence of intrinsically disordered regions (IDRs). Notably, the aggregation propensity was not significantly changed by a removal of IDRs in model IDR-containing proteins, suggesting that the properties of ordered regions in these proteins are the dominant factors for aggregate formation. We also found that the proteins with longer IDRs were disfavored by E. coli chaperonin GroEL/ES, whereas both bacterial and yeast Hsp70/40 chaperones have a strong aggregation-prevention effect even for proteins possessing IDRs. These results imply that a key determinant to discriminate the eukaryotic proteomes from the prokaryotic proteomes in terms of protein folding would be the attachment of IDRs.
DOI: 10.6084/m9.figshare.7996385
title: Additive prognostic value of Minkowski functionals in glioblastoma

description: Minkowski functionals extracted from peritumoral edema of glioblastoma patients (n=113)<br>
DOI: 10.6084/m9.figshare.7996394
title: Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins

description: Protein folding often competes with intermolecular aggregation, which in most cases irreversibly impairs protein function, as ex- emplified by the formation of inclusion bodies. Although it has been empirically determined that some proteins tend to aggregate, the relationship between the protein aggregation propensities and the primary sequences remains poorly understood. Here, we indi- vidually synthesized the entire ensemble of Escherichia coli pro- teins by using an in vitro reconstituted translation system and analyzed the aggregation propensities. Because the reconstituted translation system is chaperone-free, we could evaluate the inher- ent aggregation propensities of thousands of proteins in a trans- lation-coupled manner. A histogram of the solubilities, based on data from 3,173 translated proteins, revealed a clear bimodal distribution, indicating that the aggregation propensities are not evenly distributed across a continuum. Instead, the proteins can be categorized into 2 groups, soluble and aggregation-prone pro- teins. The aggregation propensity is most prominently correlated with the structural classification of proteins, implying that the prediction of aggregation propensity requires structural informa- tion about the protein.
DOI: 10.6084/m9.figshare.7996346
title: Translation-coupled protein folding assay using a protease to monitor the folding status

description: Protein folding is an essential prerequisite for proteins to execute nearly all cellular functions. There is a growing demand for a simple and robust method to investigate protein folding on a large-scale under the same conditions. We previously developed a global folding assay system, in which proteins translated using an Escherichia coli-based cell-free translation system are centrifuged to quantitate the supernatant fractions. Although the assay is based on the assumption that the supernatants contain the folded native states, the supernatants also include nonnative unstructured proteins. In general, proteases recognize and degrade unstructured proteins, and thus we used a protease to digest the unstructured regions to monitor the folding status. The addition of Lon protease during the translation of proteins unmasked subfractions, not only in the soluble fractions but also in the aggregation-prone fractions. We translated ~90 E. coli proteins in the protease-inclusion assay, in the absence and presence of chaperones. The folding assay, which sheds light on the molecular mechanisms underlying the aggregate formation and the chaperone effects, can be applied to a large-scale analysis.<br>
DOI: 10.6084/m9.figshare.7996352
title: Digital design of eating disorder treatments: A systematic review and meta-analysis

description: The current review and meta-analysis aimed to determine which components of web-based interventions are associated with higher attrition and improved therapeutic outcome in eating disorder treatment. A systematic of electronic databases were searched for published studies of web-based interventions for eating disorders and a meta-analysis of the final included studies was conducted. Each intervention was coded across four dimensions including multimedia channels, automated feedback, and technological device. A final 23 studies were included in the review. The results of meta-regressions indicated that higher scores on the multimedia subscale were associated with greater eating disorder symptom improvement in treatment groups. Conversely, higher scores on the feedback subscale were associated with greater reductions in eating disorder psychopathology in the control group. Other intervention components were not associated with treatment outcome or dropout. <br>
DOI: 10.6084/m9.figshare.7996346.v1
title: Translation-coupled protein folding assay using a protease to monitor the folding status

description: Protein folding is an essential prerequisite for proteins to execute nearly all cellular functions. There is a growing demand for a simple and robust method to investigate protein folding on a large-scale under the same conditions. We previously developed a global folding assay system, in which proteins translated using an Escherichia coli-based cell-free translation system are centrifuged to quantitate the supernatant fractions. Although the assay is based on the assumption that the supernatants contain the folded native states, the supernatants also include nonnative unstructured proteins. In general, proteases recognize and degrade unstructured proteins, and thus we used a protease to digest the unstructured regions to monitor the folding status. The addition of Lon protease during the translation of proteins unmasked subfractions, not only in the soluble fractions but also in the aggregation-prone fractions. We translated ~90 E. coli proteins in the protease-inclusion assay, in the absence and presence of chaperones. The folding assay, which sheds light on the molecular mechanisms underlying the aggregate formation and the chaperone effects, can be applied to a large-scale analysis.<br>
DOI: 10.6084/m9.figshare.7996385.v1
title: Additive prognostic value of Minkowski functionals in glioblastoma

description: Minkowski functionals extracted from peritumoral edema of glioblastoma patients (n=113)<br>
DOI: 10.6084/m9.figshare.7996331
title: A novel Single-chain Enzyme Complex with chain-reaction properties Rapidly Producing Thromboxane A2 and Exhibiting Powerful Anti-Bleeding Functions

description: Figures of the paper in JCMM
DOI: 10.6084/m9.figshare.7996331.v1
title: A novel Single-chain Enzyme Complex with chain-reaction properties Rapidly Producing Thromboxane A2 and Exhibiting Powerful Anti-Bleeding Functions

description: Figures of the paper in JCMM
DOI: 10.6084/m9.figshare.7996304
title: Crater catalog

description: A list of polar craters on the Moon and Mercury, latitudes &gt; 75 (Mercury) and &gt;60 (the Moon), diameters ~2-15 km.
DOI: 10.6084/m9.figshare.7996328.v1
title: Jianfengling Sapling Functional Traits from 6.6 Km transect

description: Data collected during the summer of 2017 in Jianfengling, Hainan Island, China. Juvenile tropical trees, sampled for leaves and roots. Leaves and roots scanned, dried and weighed. Morphological traits quantified with WinRhizo and WinFolia. Soil collected, sieved and sent for analysis by the Guangzhou Xinhua Agricultural Limited Company. Plant functional trait and soil data shared.
DOI: 10.6084/m9.figshare.7996241
title: CCDB_3770.jpg

description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining.
DOI: 10.6084/m9.figshare.7996244
title: CCDB_3771.jpg

description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining.