cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15151/esrf-es-1119944268
title: The Institute of Structural and Molecular Biology (ISMB) application for beam time, comprising groups from Birkbeck College, UCL and the Que

description: The ISMB spans Birkbeck and UCL with researchers in the core Departments at Birkbeck Biological Sciences and several UCL Research Departments. Research groups from Queen Mary University of London (QMUL) and Kingston University (KU) are joint co-applicants as they have strong links and collaborations with groups from ISMB. All groups share common interests in disciplines including structural, chemical, molecular and cell biology; using multidisciplinary andmultiscalar approaches. ISMB, UCL, QMUL and KU investigators, ranging from early-career research fellows to internationally-established senior academics, apply X-ray crystallography carried out mainly at our Wellcome funded facility at Birkbeck, as an essential method enabling: i) description of the atomic-level mechanistic details of macromolecules and macromolecular machines, and ii) structure-based drug discovery, while iii) complementing and supporting cryoelectron microscopy (cryo-EM) projects.
DOI: 10.15151/esrf-es-1300473354
title: XRDCT of Dried cement

description: XRDCT of Dried cement
DOI: 10.15151/esrf-es-1229949840
title: Polymeric nanogels for targeted drug delivery

description: Polymeric nanogels (NGs) have gained increasing interest as smart nanomaterials for drug delivery purposes. However, some aspects on the effective conformational structure and organization of their building blocks, and their behavior at the submicron scale within the biological compartments are not fully detailed yet. This limits the use of NGs in clinical scenarios. We proposed the formulation of hyaluronic acid-polyethylenimine (HA-PEI) NGs for CD44-targeting therapy in ovarian cancer. The aim of the proposal is a deep structural investigation of HA-PEI NGs by SAXS/WAXS techniques as a function of synthesis methods, drug loading, and environmental conditions. The stability/degradation trend and the interaction with lipid model membranes will also be addressed, helping the optimization of the design and engineering of these materials for biomedical applications.
DOI: 10.15151/esrf-es-1229950544
title: Synergistic use of serial and powder crystallography on proteins

description: This proposal focuses on the synergistic use of serial crystallography and powder diffraction for extracting domain size and strain estimates and phase weight estimates from microcrystalline protein powders. Serial diffraction images only record partial reflections and downstream processing requires a large number of independent observations per reflection to reliably converge and estimate the full reflection intensity. Parameters such as mosaic domain size and strain or co-existence of multiple crystalline phases further complicate processing. Here, we propose to use high resolution powder diffraction data for extracting domain size and strain distributions and feed those parameters back to serial data processing algorithms for more reliable merging and scaling from fewer diffraction images. Improvements in protein serial data processing could yield better electron density maps that would enable resolving finer structural details, which is crucial especially in time-resolved studies.
DOI: 10.15151/esrf-es-1229952144
title: Characterization of osteosarcoma resected human tissue by using XANES at the Ca-K edges

description: The aim of this proposal is to assess bone quality of osteosarcoma resected human tissue by using μXANES at the Ca K-edges to obtain the chemical speciation of mineral bone at a spatial resolution down to the micrometric scale. This will allow to visualise and evaluate bone composition of osteosarcoma tissue and to compare the healthy control bone with OS affected tissue from the same subject. Due to its rarity, osteosarcoma is still lacking a reliable and precise chemical characterization of bone composition and the results of this proposal will help to tackle this gap. Thanks to a better understanding of bone changes in OS tissue this study could be translated into: i) pre-clinical research, ii) therapeutic strategy and iii) eventually clinical practice.
DOI: 10.15151/esrf-es-1296030017
title: RIXS investigation of Li ion battery cathodes

description: RIXS investigation of Li ion battery cathodes
DOI: 10.15151/esrf-es-1296368619
title: Test of a 150 MP detector for X-ray tomography

description: Real-life tests of a large detector chip for multiscale tomography of diverse samples.
DOI: 10.5281/zenodo.8176609
title: Stability of neutrino oscillation parameters at low energy scale with the variations of SUSY breaking scale under Renormalisation Group Equations

description: <pre>We discuss the stability of the neutrino oscillation parameters at low energy scale including self-complementarity (SC) relations among mixing angles under radiative corrections with the variation of SUSY breaking scale ($m_s$) in both normal and inverted hierarchical cases. We observe that the neutrino oscillation parameters including the SC relation maintains stability at the electroweak scale within $1\sigma$ range of the latest global fit data. NH case maintains more stability than IH case. All the numerical values related to the absolute neutrino masses viz., $\Sigma |m_i|$, $m_{\beta}$ and $m_{ \beta \beta}$ are found to lie below the observational upper bound.</pre> <pre> </pre> <pre> </pre>
DOI: 10.5281/zenodo.8176608
title: Stability of neutrino oscillation parameters at low energy scale with the variations of SUSY breaking scale under Renormalisation Group Equations

description: <pre>We discuss the stability of the neutrino oscillation parameters at low energy scale including self-complementarity (SC) relations among mixing angles under radiative corrections with the variation of SUSY breaking scale ($m_s$) in both normal and inverted hierarchical cases. We observe that the neutrino oscillation parameters including the SC relation maintains stability at the electroweak scale within $1\sigma$ range of the latest global fit data. NH case maintains more stability than IH case. All the numerical values related to the absolute neutrino masses viz., $\Sigma |m_i|$, $m_{\beta}$ and $m_{ \beta \beta}$ are found to lie below the observational upper bound.</pre> <pre> </pre> <pre> </pre>
DOI: 10.11588/data/nsmm6p/3rdddk
title: Metadata_TSF.txt

description: :unav
DOI: 10.11588/data/nsmm6p/5ltvu0
title: target_very_big_Kunene_VH.csv

description: :unav
DOI: 10.11588/data/nsmm6p/jgmzb2
title: training_VH_Kunene.csv

description: :unav
DOI: 10.11588/data/nsmm6p/ffoiyt
title: time_series_forest.py

description: :unav
DOI: 10.11588/data/nsmm6p/zyr4io
title: Prediction_VH_Kunene-2.tab

description: :unav
DOI: 10.11588/data/nsmm6p/unx8h1
title: Prediction_VH_Kunene.csv

description: :unav
DOI: 10.11588/data/nsmm6p/uo2ulg
title: Prediction_VH_Kunene-1.csv

description: :unav
DOI: 10.5281/zenodo.8176631
title: Stability of neutrino oscillation parameters at low energy scale with the variations of SUSY breaking scale under Renormalisation Group Equations

description: <pre>We discuss the stability of the neutrino oscillation parameters at low energy scale including self-complementarity (SC) relations among mixing angles under radiative corrections with the variation of SUSY breaking scale ($m_s$) in both normal and inverted hierarchical cases. We observe that the neutrino oscillation parameters including the SC relation maintains stability at the electroweak scale within $1\sigma$ range of the latest global fit data. NH case maintains more stability than IH case. All the numerical values related to the absolute neutrino masses viz., $\Sigma |m_i|$, $m_{\beta}$ and $m_{ \beta \beta}$ are found to lie below the observational upper bound.</pre>
DOI: 10.5281/zenodo.8176630
title: Stability of neutrino oscillation parameters at low energy scale with the variations of SUSY breaking scale under Renormalisation Group Equations

description: <pre>We discuss the stability of the neutrino oscillation parameters at low energy scale including self-complementarity (SC) relations among mixing angles under radiative corrections with the variation of SUSY breaking scale ($m_s$) in both normal and inverted hierarchical cases. We observe that the neutrino oscillation parameters including the SC relation maintains stability at the electroweak scale within $1\sigma$ range of the latest global fit data. NH case maintains more stability than IH case. All the numerical values related to the absolute neutrino masses viz., $\Sigma |m_i|$, $m_{\beta}$ and $m_{ \beta \beta}$ are found to lie below the observational upper bound.</pre>
DOI: 10.5281/zenodo.7535903
title: Dataset for "Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system"

description: Numerical results for "<strong>Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system</strong>".
DOI: 10.5281/zenodo.8137770
title: Dataset for "Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system"

description: Numerical results for "<strong>Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system</strong>".
DOI: 10.5281/zenodo.7535902
title: Dataset for "Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system"

description: Numerical results for "<strong>Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system</strong>".
DOI: 10.5281/zenodo.8176640
title: Dataset for "Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system"

description: Numerical results for "<strong>Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system</strong>".
DOI: 10.5519/qd.w5ax9fhe
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (24 records)
DOI: 10.6084/m9.figshare.21155786
title: Gene Expression Analyses of Mutant <i>Flammulina velutipes</i> (Enokitake Mushroom) with Clogging Phenomenon

description: Regulation of proper gene expression is important for cellular and organismal survival, maintenance, and growth. Abnormal gene expression, even for a single critical gene, can thwart cellular integrity and normal physiology to cause diseases, aging, and death. Therefore, gene expression profiling serves as a powerful tool to understand the pathology of diseases and to cure them. In this study, the difference in gene expression in <i>Flammulina velutipes</i> was compared between the wild type (WT) mushroom and the mutant one with clogging phenomenon. Differentially expressed transcripts were screened to identify the candidate genes responsible for the mutant phenotype using the DNA microarray analysis. A total of 88 genes including 60 upregulated and 28 downregulated genes were validated using the real-time quantitative PCR analysis. In addition, proteomic differences between the WT and mutant mushroom were analyzed using two–dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Interestingly, the genes identified by these genomic and proteomic analyses were involved in stress response, translation, and energy/sugar metabolism, including HSP70, elongation factor 2, and pyruvate kinase. Together, our data suggest that the aberrant expression of these genes attributes to the mutant clogging phenotype. We propose that these genes can be targeted to foster normal growth in <i>F. velutipes</i>.
DOI: 10.6084/m9.figshare.21476845
title: Mitochondrial Effects on the Physiological Characteristics of <i>Lentinula edodes</i>

description: In the mating of filamentous basidiomycetes, dikaryotic mycelia are generated through the reciprocal movement of nuclei to a monokaryotic cytoplasm where a nucleus of compatible mating type resides, resulting in the establishment of two different dikaryotic strains having the same nuclei but different mitochondria. To better understand the role of mitochondria in mushrooms, we created four sets of dikaryotic strains of <i>Lentinula edodes</i>, including B2 × E13 (B2 side) and B2 × E13 (E13 side), B5 × E13 (B5 side) and B5 × E13 (E13 side), E8 × H3 (E8 side) and E8 × H3 (H3 side), and K3 × H3 (K3 side) and K3 × H3 (H3 side). The karyotypes and mitochondrial types of the dikaryotic strains were successfully identified by the <i>A</i> mating type markers and the mitochondrial variable length tandem repeat markers, respectively. Comparative analyses of the dikaryotic strains on the mycelial growth, substrate browning, fruiting characteristics, and mitochondrial gene expression revealed that certain mitochondria are more effective in the mycelial growth and the production of fruiting body, possibly through the activated energy metabolism. Our findings indicate that mitochondria affect the physiology of dikaryotic strains having the same nuclear information and therefore a selection strategy aimed at mitochondrial function is needed in the development of new mushroom strain.
DOI: 10.6084/m9.figshare.21476845.v1
title: Mitochondrial Effects on the Physiological Characteristics of <i>Lentinula edodes</i>

description: In the mating of filamentous basidiomycetes, dikaryotic mycelia are generated through the reciprocal movement of nuclei to a monokaryotic cytoplasm where a nucleus of compatible mating type resides, resulting in the establishment of two different dikaryotic strains having the same nuclei but different mitochondria. To better understand the role of mitochondria in mushrooms, we created four sets of dikaryotic strains of <i>Lentinula edodes</i>, including B2 × E13 (B2 side) and B2 × E13 (E13 side), B5 × E13 (B5 side) and B5 × E13 (E13 side), E8 × H3 (E8 side) and E8 × H3 (H3 side), and K3 × H3 (K3 side) and K3 × H3 (H3 side). The karyotypes and mitochondrial types of the dikaryotic strains were successfully identified by the <i>A</i> mating type markers and the mitochondrial variable length tandem repeat markers, respectively. Comparative analyses of the dikaryotic strains on the mycelial growth, substrate browning, fruiting characteristics, and mitochondrial gene expression revealed that certain mitochondria are more effective in the mycelial growth and the production of fruiting body, possibly through the activated energy metabolism. Our findings indicate that mitochondria affect the physiology of dikaryotic strains having the same nuclear information and therefore a selection strategy aimed at mitochondrial function is needed in the development of new mushroom strain.
DOI: 10.5281/zenodo.8176672
title: Simulated spatially explicit dataset (300 m) on future forest cover changes in Southeast Asia projected under the baseline shared socioeconomic pathways

description: This is a simulated spatially explicit dataset on future forest cover changes in Southeast Asia projected under the baseline shared socioeconomic pathways. It includes six raster maps at a spatial resolution of 300 m: (1) 2015 baseline forest and non-forest map; (2) SSP1 2050 projected net forest gain map; (3) SSP2 2050 projected net forest gain map; (4) SSP3 2050 projected net forest loss map; (5) SSP4 2050 projected net forest gain map; and SSP5 2050 projected net forest loss map. This dataset is the result of a study published in Nature Communications (2019) (https://doi.org/10.1038/s41467-019-09646-4).
DOI: 10.5281/zenodo.8162178
title: Simulated spatially explicit dataset (300 m) on future forest cover changes in Southeast Asia projected under the baseline shared socioeconomic pathways

description: This is a simulated spatially explicit dataset on future forest cover changes in Southeast Asia projected under the baseline shared socioeconomic pathways. It includes six raster maps at a spatial resolution of 300 m: (1) 2015 baseline forest and non-forest map; (2) SSP1 2050 projected net forest gain map; (3) SSP2 2050 projected net forest gain map; (4) SSP3 2050 projected net forest loss map; (5) SSP4 2050 projected net forest gain map; and SSP5 2050 projected net forest loss map. This dataset is the result of a study published in Nature Communications (2019) (https://doi.org/10.1038/s41467-019-09646-4).
DOI: 10.5281/zenodo.7675570
title: BSpell: A CNN-Blended BERT Based Bengali Spell Checker Dataset

description: Bengali typing is mostly performed using English keyboard and can be highly erroneous due to the presence of compound and similarly pronounced letters. Spelling correction of a misspelled word requires understanding of word typing pattern as well as the context of the word usage. A specialized BERT model named BSpell has been proposed in this paper targeted towards word for word correction in sentence level. BSpell contains an end-to-end trainable CNN sub-model named SemanticNet along with specialized auxiliary loss. This allows BSpell to specialize in highly inflected Bengali vocabulary in the presence of spelling errors. furthermore, a hybrid pretraining scheme has been proposed for BSpell that combines word level and character level masking. Comparison on two Bengali and one Hindi spelling correction dataset shows the superiority of our proposed approach.
DOI: 10.5281/zenodo.7675569
title: BSpell: A CNN-Blended BERT Based Bengali Spell Checker Dataset

description: Bengali typing is mostly performed using English keyboard and can be highly erroneous due to the presence of compound and similarly pronounced letters. Spelling correction of a misspelled word requires understanding of word typing pattern as well as the context of the word usage. A specialized BERT model named BSpell has been proposed in this paper targeted towards word for word correction in sentence level. BSpell contains an end-to-end trainable CNN sub-model named SemanticNet along with specialized auxiliary loss. This allows BSpell to specialize in highly inflected Bengali vocabulary in the presence of spelling errors. furthermore, a hybrid pretraining scheme has been proposed for BSpell that combines word level and character level masking. Comparison on two Bengali and one Hindi spelling correction dataset shows the superiority of our proposed approach.
DOI: 10.18712/nsd-nsd3121-v1
title: Democratic Urban Development in the Digital Age (DEMUDIG)

description: The data was collected in connection with the DEMUDIG project which lasted from 01.07.2018-31.03.2022. The project compared citizen participation in urban development in Oslo, Madrid and Melbourne. The project was about participation and involvement, and studied how citizens and other stakeholders engaged and what the authorities did to obtain input from the population. It focused especially on participation via websites, apps and social media. The project was also concerned with what happens to the input when the participation process is completed and the policy is to be implemented.
DOI: 10.25345/c52n4zt8d
title: MassIVE MSV000092508 - Overcoming therapeutic resistance in GBM
title: To reveal specific mechanisms of drug resistance about bevacizumab treatment in GBM patients who have prolonged disease free survival (DFS), but retained overall survival (OV), we established systemic drug-resistance murine GBM model in the context of tumor evolutionary with time series brain tissue collection. And to trace the change of specific functional molecules along the bevacizumab resistance, we performed LC-MS/MS-based global, phospho-proteomic analysis and NGS-based transcriptomic analysis using the time series murine GBM model.
DOI: 10.6084/m9.figshare.23735370
title: Supplementary Material for: Impact of ‘Black Race’ Coefficient in eGFR on Our Community and Medical Education

description: Introduction: The use of race in estimation of glomerular filtration rate (eGFR) started a critical national conversation on numerous areas of medicine touched by racism; with a call for removal of race from calculation of eGFR. We scrutinized use of ‘Black race’ coefficient in MDRD eGFR calculation and consequence of its use on our local community in SW Michigan. Methods: A cross-sectional analysis of de-identified electronic health record (EHR) data from routine outpatient primary care visits, from 1/1/2019 to 12/31/2019 included variables such as age, race, gender, serum creatinine levels and calculated eGFRs (if any), using Chi-square tests for association and Wald-approximation 95% confidence interval. During the data collection period in 2019, both hospital systems and the outpatient clinic site were all using MDRD. Results: eGFR and associated CKD stage were calculated for 131,863 patients. Chi-square tests found significant differences in rates of CKD stages 3,4 and 5 between ‘Black’ and ‘not Black’. And, the 95% confidence interval for the proportion of Black patients who would advance to the next stage of CKD upon ignoring ‘Black race’ (using Wald-approximated Confidence Interval for binomial proportion) is between 41.1% and 43.0%. Discussion: The eGFR calculations which place Black patients in lower CKD stages initially may deprive them of important treatment and referral early in their disease course. Removal of the Black race coefficient allows for referral to a nephrologist, Medicare coverage, and the potential need for transplant and/or dialysis. Conclusion: Our analysis demonstrates the impact removal of ‘black race’ coefficient from MDRD eGFR calculation could have on our community.
DOI: 10.6084/m9.figshare.23735382
title: Supplementary Material for: Impact of ‘Black Race’ Coefficient in eGFR on Our Community and Medical Education

description: Introduction: The use of race in estimation of glomerular filtration rate (eGFR) started a critical national conversation on numerous areas of medicine touched by racism; with a call for removal of race from calculation of eGFR. We scrutinized use of ‘Black race’ coefficient in MDRD eGFR calculation and consequence of its use on our local community in SW Michigan. Methods: A cross-sectional analysis of de-identified electronic health record (EHR) data from routine outpatient primary care visits, from 1/1/2019 to 12/31/2019 included variables such as age, race, gender, serum creatinine levels and calculated eGFRs (if any), using Chi-square tests for association and Wald-approximation 95% confidence interval. During the data collection period in 2019, both hospital systems and the outpatient clinic site were all using MDRD. Results: eGFR and associated CKD stage were calculated for 131,863 patients. Chi-square tests found significant differences in rates of CKD stages 3,4 and 5 between ‘Black’ and ‘not Black’. And, the 95% confidence interval for the proportion of Black patients who would advance to the next stage of CKD upon ignoring ‘Black race’ (using Wald-approximated Confidence Interval for binomial proportion) is between 41.1% and 43.0%. Discussion: The eGFR calculations which place Black patients in lower CKD stages initially may deprive them of important treatment and referral early in their disease course. Removal of the Black race coefficient allows for referral to a nephrologist, Medicare coverage, and the potential need for transplant and/or dialysis. Conclusion: Our analysis demonstrates the impact removal of ‘black race’ coefficient from MDRD eGFR calculation could have on our community.