cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24139083.v1
title: Supplementary Material for: Bioinformatics Analysis and Screening of Potential Target Genes Related to the Lung Cancer Prognosis

description: Objective: Several genes have been validated as molecular targets for gene therapy in lung cancer. We screened target genes that affect survival of patients with lung cancer. Methods: Data on gene expression in normal lung tissues/lung adenocarcinoma (LUAD) samples were acquired from Genotype-Tissue Expression (GTEx)/The Cancer Genome Atlas (TCGA) databases and merged to expand the sample size, followed by differential analysis of the merged expression data and acquisition of differentially expressed genes. Survival and simple Cox analyses were used to screen for genes affecting LUAD survival. Protein-protein interaction/multivariable Cox analyses were utilized, and a risk model was established. Candidate genes expression levels in cancer/paracancerous tissues of lung cancer patients, and BEAS-2B/A549/HCC95 cells were measured by RT-qPCR/Western blot. Survival analysis of candidate genes was conducted in LUAD samples collected from TCGA. Results: Among 947 genes differentially expressed in LUAD, 151 were correlated with patient survival, and 116 might act as risk factors for LUAD. The 7 identified candidate genes (TOP2A, TK1, KIF4A, ANLN, KIF2C, ASF1B, CCNB1) were high-risk genes playing possible roles in LUAD. These genes were differentially expressed in lung cancer and were associated with TNM stages (III - IV)/differentiation grade/lymph node metastasis/distant metastasis, which affected lung cancer patient survival. Conclusion: P2A, TK1, KIF4A, ANLN, KIF2C, ASF1B and CCNB1 were highly-expressed in LUAD/lung squamous cell carcinoma (LUSC) and correlated with LUAD patient survival. This study contributes to better understanding of the prognostic regulation mechanism in LUAD and the screening of target genes for clinical treatment.
DOI: 10.5281/zenodo.8345255
title: galeopsomyia_nigrocyanea_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8345254
title: galeopsomyia_nigrocyanea_spades_01.fasta.gz

description: .
DOI: 10.5517/ccdc.csd.cc2gvvgn
title: CCDC 2289922: Experimental Crystal Structure Determination

description: Related Article: H.V.P. Hollauer, R.C. Vilas Novas, G.P. Guedes, C.D. Buarque, L.B.L. Escobar|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|842|doi:10.1107/S2056989023007351
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.24139110.v1
title: Supplementary Material for: The Worsening Renal Perfusion Index predicts the prognoses of heart failure patients treated with sacubitril/valsartan

description: Introduction: Sacubitril/valsartan (S/V) reduces all-cause mortality in patients with heart failure with reduced ejection fraction (HFrEF), but it may decline their estimated glomerular filtration rates (eGFR). In addition to eGFR, this clinical study aimed to develop a blood urea nitrogen (BUN)-based index to evaluate the status of renal perfusion and then identify predictors of all-cause death or heart transplant in patients with HFrEF receiving S/V. Methods: From the recruited 291 patients with HFrEF who were prescribed S/V from March 2017 to March 2019, we collected demographic, drug history, laboratory, echocardiographic, and clinical data from one year before S/V initiation until December 2020. Regression analysis was conducted by fitting Cox’s models with time-dependent covariates for the survival time and applying the modern stepwise variable selection procedure. The smoothing spline method was used to detect nonlinearity in effect and yield optimal cut-off values for continuous covariates. Results: In the Cox’s model, decreased hemoglobin level, decreased mean left ventricular ejection fraction, declined daily dose of S/V, decreased eGFR within 3 months, and increased BUN levels within 1 month and 9 months over time were significantly associated with an increased risk of all-cause death or heart transplant in patients with HFrEF. Conclusions: Adequate maintenance of renal perfusion is crucial for the continuous use of S/V and to avoid worsening renal function in patients with HFrEF. We defined the maximum increase in BUN levels within a specified period as the Worsening Renal Perfusion Index (WRPSV Index) to capture the prognostic effect of renal hypoperfusion in patients with HFrEF.
DOI: 10.5281/zenodo.8345291
title: heliconius_charithonia_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8345290
title: heliconius_charithonia_spades_01.fasta.gz

description: .
DOI: 10.57745/ylr793
title: Relative_contributions_of_field_transport_process_Fig.4_A.5.tab

description: Data on relative contributions of the studied environmental impacts for the field, transport and dehydration processes from the cradle to the factory gate (Figure 4 of the article).
DOI: 10.57745/ixo4lk
title: LCI_Alfalfa_P2_at_field.tab

description: Data on the life cycle inventories at field for period 2 (2016-2019) studied.
DOI: 10.57745/j3xmnv
title: Alfalfa_at_time_destruction_Fig.A.1.tab

description: Data on age of alfalfa at the time of destruction (Figure A.1 of the article).
DOI: 10.57745/uc7klg
title: LCI_Alfalfa_P2_processing-1.tab

description: Alfalfa dehydration industrial process life cycle inventories data for period 2.
DOI: 10.57745/sckjgy
title: LCI_Alfalfa_P1_processing-1.tab

description: Alfalfa dehydration industrial process life cycle inventories data for period 1.
DOI: 10.57745/uja28h
title: Relative_contributions_of_field_transport_process_Fig.4_A.5-1.tab

description: Data on relative contributions of environmental impacts criteria studied in periods 1 an 2 relating to the dehydrated alfalfa production for the fonctionnal units (Figures 5a and b of the article).
DOI: 10.57745/agwebh
title: Areas_of_alfalfa_stands_cultivated_Fig.1-1.tab

description: Data on areas of alfalfa stands cultivated for dehydration (Figure 1 of the article).
DOI: 10.57745/nucb8w
title: DryMatter_protein_Electricity_Fig.3_6_A.2_A.4_A.6.tab

description: Data of dry matter yield and content, protein content, electricity and aridity index (Figures 3, A.2, A.6, A.4 and 6 of the article).
DOI: 10.57745/8exxif
title: LCI_Alfalfa_P1_at_field-1.tab

description: Data on life cycle inventories on production of alfalfa at field, for period 1 (2006-2009) studied.
DOI: 10.57745/b6bgos
title: Acronym_list.docx

description: List of acronyms used
DOI: 10.57745/4dyxeb
title: Low_calorific_value_Fig.A.3.tab

description: Data on lower calorific value of the main energy sources used during the two study periods (Figure A3 of the article)
DOI: 10.57967/hf/1112
title: global-stocktake-documents
DOI: 10.57967/hf/0842
title: global-stocktake-documents
DOI: 10.25573/data.19108310.v3
title: Bay of Panama Water Quality Monitoring Project, Summary

description: Bay of Panama water quality monitoring program. <br>Excel file summarizing the data<br>Weekly depth profile (approximately 5m intervals) using YSI EXO 2 sonde.<br>Parameters measured temperature, salinity, conductivity, pH, turbidity, chlorophyll, Dissolved Oxygen
DOI: 10.5281/zenodo.8345313
title: ormyrus_rosae_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8345312
title: ormyrus_rosae_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23735691.v2
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.23735691.v1
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.23678082.v2
title: Supplementary Material for: Quality of Life Measures in Aortic Stenosis Research: A Narrative Review

description: Background: Elderly patients with aortic stenosis (AS) not only have a reduced life expectancy but also a reduced quality of life (QoL). The benefits of an AS intervention may be considered a balance between a good QoL and a reasonably extended life. However, the different questionnaires being used to determine the QoL, were generally not developed for the specific situation of patients with AS and come with strengths and considerable weaknesses. The objective of this manuscript was to provide an overview of the available QoL instruments in AS research, describe their strengths and weaknesses, and to provide our assessment of the utility of the available scoring instruments for QoL measurements in AS. Summary: We identified and reviewed the following instruments that are used in AS research: Short Form Health Survey (SF-36/SF-12), EuroQol-5D (EQ-5D), the Illness Intrusiveness Rating Scale (IIRS), the HeartQoL, the Kansas City Cardiomyopathy Questionnaire (KCCQ), the Minnesota Living with Heart Failure Questionnaire (MLHF), the MacNew Questionnaire, and the Toronto Aortic Stenosis Quality of Life Questionnaire (TASQ). Key messages: There is no standardized assessment of QoL in patients with AS. Many different questionaires are being used, but they are rarely specific for AS. There is a need for AS specific research into the QoL of patients as life prolongation may compete for an improved QoL in this elderly patient group.
DOI: 10.6084/m9.figshare.23678082.v1
title: Supplementary Material for: Quality of Life Measures in Aortic Stenosis Research: A Narrative Review

description: Background: Elderly patients with aortic stenosis (AS) not only have a reduced life expectancy but also a reduced quality of life (QoL). The benefits of an AS intervention may be considered a balance between a good QoL and a reasonably extended life. However, the different questionnaires being used to determine the QoL, were generally not developed for the specific situation of patients with AS and come with strengths and considerable weaknesses. The objective of this manuscript was to provide an overview of the available QoL instruments in AS research, describe their strengths and weaknesses, and to provide our assessment of the utility of the available scoring instruments for QoL measurements in AS. Summary: We identified and reviewed the following instruments that are used in AS research: Short Form Health Survey (SF-36/SF-12), EuroQol-5D (EQ-5D), the Illness Intrusiveness Rating Scale (IIRS), the HeartQoL, the Kansas City Cardiomyopathy Questionnaire (KCCQ), the Minnesota Living with Heart Failure Questionnaire (MLHF), the MacNew Questionnaire, and the Toronto Aortic Stenosis Quality of Life Questionnaire (TASQ). Key messages: There is no standardized assessment of QoL in patients with AS. Many different questionaires are being used, but they are rarely specific for AS. There is a need for AS specific research into the QoL of patients as life prolongation may compete for an improved QoL in this elderly patient group.
DOI: 10.6084/m9.figshare.23946960.v1
title: Supplementary Material for: Glomeruli count and arterial injury in real-time ultrasound-guided needle kidney biopsy specimens: Adequacy of three approaches for pig kidneys

description: Introduction. Real-time ultrasound-guided percutaneous kidney biopsy is essential for diagnosis and treatment planning; nonetheless, the optimal puncture approach has yet to be established. In vivo, performing different approaches on the same patient at once is not possible. This study aimed to determine the impact of different approaches on the number of obtained glomeruli and their potential to cause arterial injury using pig kidneys, which are similar to humans. Methods. A total of 120 pig kidneys (60 right-sided kidneys and 60 left-sided kidneys) for research were obtained from a slaughterhouse. The specimens were collected from the lower pole on the sagittal plane of the kidney using three different approaches on the same kidney: Caudocranial approach, caudal to cranial; Craniocaudal approach, cranial to caudal; and Vertical approach, through the surface cortex. Five blinded pediatric nephrologists assessed the number of glomeruli and arterial injuries. Results. Overall, 360 specimens were collected from the kidneys through biopsy using a 16-gauge needle (mean vertical kidney length, 11.2 ± 0.7 cm; mean depth, 3.47 ± 0.23 cm). No significant difference in the incidence of arterial injury was observed between the three approaches (Caudocranial vs. Craniocaudal vs. Vertical approaches: 78% vs. 87% vs. 87%, P = 0.14). In contrast, the Vertical approach retrieved significantly more glomeruli than the Caudocranial and Craniocaudal approaches (Caudocranial approach: 7.5 ± 2.8, Craniocaudal approach: 7.8 ± 2.7, and Vertical approach: 8.9 ± 3.3, P &lt; 0.001). Conclusions. Considering its efficacy and safety profile, the Vertical approach may be preferred, as more glomeruli can be obtained without increasing the incidence of arterial injury. Although the results cannot be directly extrapolated to humans due to the differences between species, they still offer important insights into the characteristics of each approach.
DOI: 10.5517/ccdc.csd.cc22b8yn
title: CCDC 1916511: Experimental Crystal Structure Determination

description: Related Article: Hao Zhang, Frank Rominger, Uwe H. F. Bunz, Jan Freudenberg|2019|Chem.-Eur.J.|25|11218|doi:10.1002/chem.201902272
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: 10.5517/ccdc.csd.cc22b8zp
title: CCDC 1916512: Experimental Crystal Structure Determination

description: Related Article: Hao Zhang, Frank Rominger, Uwe H. F. Bunz, Jan Freudenberg|2019|Chem.-Eur.J.|25|11218|doi:10.1002/chem.201902272
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: 10.5281/zenodo.8345319
title: Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis

description: This dataset contains the raw data that lie at the basis of the results discussed in <strong>Chapter 5: Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis </strong>of the PhD thesis of Amber Bernauw. This chapter is also published as an article at MicrobiologyOpen (https://doi.org/10.1002/mbo3.1356).
DOI: 10.5281/zenodo.8345318
title: Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis

description: This dataset contains the raw data that lie at the basis of the results discussed in <strong>Chapter 5: Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis </strong>of the PhD thesis of Amber Bernauw. This chapter is also published as an article at MicrobiologyOpen (https://doi.org/10.1002/mbo3.1356).
DOI: 10.5281/zenodo.8345331
title: octopus_jollyorum_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8345330
title: octopus_jollyorum_spades_01.fasta.gz

description: .
DOI: 10.18112/openneuro.ds004754.v1.0.0
title: SpinalExpect_NonInvasive
DOI: 10.18742/23905944
title: Data for MACE Dissertation: 'Identity formation within an undergraduate longitudinal General Practice placement: A Case Study Exploration through the Lens of Communities of Practice'

description: Data collected for Masters in Clinical Education to address the following inquiry: <br>My research aim is therefore to explore the role of a longitudinal GP placement in medical students’ professional identity development in the early years of medical school.My research will use 4 specific sub-questions to focus it:· How do students undertaking an undergraduate longitudinal GP placement participate and learn within Communities of Practice?· What do students and tutors report about the process and extent of student's identity formation within the GP longitudinal placement?· What factors are perceived to bear the greatest impact on student learning and identity formation within a Community of Practice?· What are students’ and tutors’ perceptions of the extent of student participation and membership of the GP Community of Practice? How far are student and tutor views aligned and what are the implications of this alignment or lack of alignment?
DOI: 10.15156/bio/sh1340458.08fu
title: SH1340458.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2020680.08fu
title: SH2020680.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2020681.08fu
title: SH2020681.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.