cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7957688.v1
title: <i>Bacillus cereus</i> biofilm formation on central venous catheters of hospitalised cardiac patients

description: Formation of bacterial biofilms is a risk with many <i>in situ</i> medical devices. Biofilm-forming <i>Bacillus</i> species are associated with potentially life-threatening catheter-related blood stream infections in immunocompromised patients. Here, bacteria were isolated from biofilm-like structures within the lumen of central venous catheters (CVCs) from two patients admitted to cardiac hospital wards. Isolates belonged to the <i>Bacillus cereus</i> group, exhibited strong biofilm formation propensity, and mapped phylogenetically close to the <i>B. cereus</i> emetic cluster. Together, whole genome sequencing and quantitative PCR confirmed that the isolates constituted the same strain and possessed a range of genes important for and up-regulated during biofilm formation. Antimicrobial susceptibility testing demonstrated resistance to trimethoprim-sulphamethoxazole, clindamycin, penicillin and ampicillin. Inspection of the genome revealed several chromosomal β-lactamase genes and a sulphonamide resistant variant of <i>folP</i>. This study clearly shows that <i>B. cereus</i> persisting in hospital ward environments may constitute a risk factor from repeated contamination of CVCs.
DOI: 10.6084/m9.figshare.7957652
title: Replication Package for Task Description Granularity Experiment [TSE-2018-06-0206]

description: This is replication package for task description granularity experiment conducted in University of Oulu. The package includes the necessary materials for replicating the experiment. In addition, data and analysis scripts for the original experiment are included. <br><b>Experiment Materials:</b>- Experiment protocol- Programming task descriptions- Project templates for Eclipse IDE - Acceptance test suites- Data extraction and intervention protocols- Template for data extraction- Survey form for demographic information- Survey form for task and performance evaluation<br><b>Data and Analysis Files:</b>- Raw data files in CSV and R data formats- Data analysis scripts for R- Data analysis report<br>
DOI: 10.6084/m9.figshare.12878353.v1
title: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

description: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
DOI: 10.6084/m9.figshare.12878353.v3
title: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

description: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
DOI: 10.6084/m9.figshare.12878353.v2
title: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

description: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
DOI: 10.6084/m9.figshare.12878353.v4
title: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

description: Additional file of Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
DOI: 10.6084/m9.figshare.7957643.v1
title: I COUGH extended data

description: This discusses the questions asked to the nurses during the study and also pattern of scoring the answers with reference to the variables within the I COUGH acronym.
DOI: 10.6084/m9.figshare.12878356
title: Additional file 1 of Copy number variation of microRNA genes in the human genome

description: Additional file 1:SNPs identified in pre-miRNA sequences. Excel table containing list of SNPs identified in annotated pre-miRNA sequences. (XLS 36 KB)
DOI: 10.6084/m9.figshare.12878359
title: Additional file 2 of Copy number variation of microRNA genes in the human genome

description: Additional file 2:miRNA identified in CNV regions. Excel table containing list of pre-miRNA annotated sequences identified in 'DGV-deposited' CNVs. (XLS 50 KB)
DOI: 10.6084/m9.figshare.12878368.v1
title: Additional file 5 of Copy number variation of microRNA genes in the human genome

description: Additional file 5:miRNAs located in chromosomal regions implicated in microdeletion/microduplication syndromes. Excel table containing list of miRNAs located in chromosomal regions implicated in microdeletion/microduplication syndromes (DECYPHER v5.0 [50]). (XLS 20 KB)
DOI: 10.6084/m9.figshare.12878356.v1
title: Additional file 1 of Copy number variation of microRNA genes in the human genome

description: Additional file 1:SNPs identified in pre-miRNA sequences. Excel table containing list of SNPs identified in annotated pre-miRNA sequences. (XLS 36 KB)
DOI: 10.6084/m9.figshare.12878365.v1
title: Additional file 4 of Copy number variation of microRNA genes in the human genome

description: Additional file 4:miRNAs located in CNVs with well defined breakpoints. Excel table showing characteristics of miRNAs located in CNVs with well defined breakpoints. (XLS 14 KB)
DOI: 10.6084/m9.figshare.12878368
title: Additional file 5 of Copy number variation of microRNA genes in the human genome

description: Additional file 5:miRNAs located in chromosomal regions implicated in microdeletion/microduplication syndromes. Excel table containing list of miRNAs located in chromosomal regions implicated in microdeletion/microduplication syndromes (DECYPHER v5.0 [50]). (XLS 20 KB)
DOI: 10.6084/m9.figshare.12878365
title: Additional file 4 of Copy number variation of microRNA genes in the human genome

description: Additional file 4:miRNAs located in CNVs with well defined breakpoints. Excel table showing characteristics of miRNAs located in CNVs with well defined breakpoints. (XLS 14 KB)
DOI: 10.6084/m9.figshare.12878377.v1
title: Additional file of Copy number variation of microRNA genes in the human genome

description: Additional file of Copy number variation of microRNA genes in the human genome
DOI: 10.6084/m9.figshare.12878377.v2
title: Additional file of Copy number variation of microRNA genes in the human genome

description: Additional file of Copy number variation of microRNA genes in the human genome
DOI: 10.6084/m9.figshare.12878377.v4
title: Additional file of Copy number variation of microRNA genes in the human genome

description: Additional file of Copy number variation of microRNA genes in the human genome
DOI: 10.6084/m9.figshare.12878359.v1
title: Additional file 2 of Copy number variation of microRNA genes in the human genome

description: Additional file 2:miRNA identified in CNV regions. Excel table containing list of pre-miRNA annotated sequences identified in 'DGV-deposited' CNVs. (XLS 50 KB)
DOI: 10.6084/m9.figshare.12878377.v5
title: Additional file of Copy number variation of microRNA genes in the human genome

description: Additional file of Copy number variation of microRNA genes in the human genome
DOI: 10.6084/m9.figshare.7957508
title: Inferring differential behavior between giant ground sloth adults and juveniles through scapula morphology

description: Animals with large differences in body size between adults and juveniles will often exhibit differences in behavior through ontogeny, and these behavioral differences can sometimes have direct effects on skeletal morphology. Scapula shape has been shown in several groups to be highly influenced by function and in some groups to be a good indicator of body size. <i>Megalonyx</i> and <i>Paramylodon</i>, two of the most common and widespread of the North American Plio-Pleistocene giant ground sloths, had overlapping temporal and geographic ranges. However, they have few co-occurrences in the fossil record. In this study, the scapulae of juvenile and adult <i>Megalonyx jeffersonii</i> and <i>Paramylodon harlani</i> were analyzed using geometric morphometrics and compared with those of the two genera of modern tree sloths, <i>Bradypus</i> and <i>Choloepus</i>. The ground sloths have significantly different scapula shapes from each other, as do the tree sloths. The scapula shapes between juveniles and adults of each genus are also significantly different from each other, with the scapulae of the juveniles of each species more circular in appearance than the more ovoid ones in adults. All four genera show significant allometry, but it is more apparent in adults than juveniles. However, there is no difference in nonallometric shape between adults and juveniles or between each pair of genera. The ground sloths exhibit similar changes in ontogeny to those observed in modern sloths, indicating that ground sloth juveniles may have engaged in similar behaviors to those of modern sloths, such as clinging to their mothers for transportation. Ground sloth juveniles also possess morphological traits that have been linked with semiarboreal behaviors.
DOI: 10.6084/m9.figshare.7957508.v1
title: Inferring differential behavior between giant ground sloth adults and juveniles through scapula morphology

description: Animals with large differences in body size between adults and juveniles will often exhibit differences in behavior through ontogeny, and these behavioral differences can sometimes have direct effects on skeletal morphology. Scapula shape has been shown in several groups to be highly influenced by function and in some groups to be a good indicator of body size. <i>Megalonyx</i> and <i>Paramylodon</i>, two of the most common and widespread of the North American Plio-Pleistocene giant ground sloths, had overlapping temporal and geographic ranges. However, they have few co-occurrences in the fossil record. In this study, the scapulae of juvenile and adult <i>Megalonyx jeffersonii</i> and <i>Paramylodon harlani</i> were analyzed using geometric morphometrics and compared with those of the two genera of modern tree sloths, <i>Bradypus</i> and <i>Choloepus</i>. The ground sloths have significantly different scapula shapes from each other, as do the tree sloths. The scapula shapes between juveniles and adults of each genus are also significantly different from each other, with the scapulae of the juveniles of each species more circular in appearance than the more ovoid ones in adults. All four genera show significant allometry, but it is more apparent in adults than juveniles. However, there is no difference in nonallometric shape between adults and juveniles or between each pair of genera. The ground sloths exhibit similar changes in ontogeny to those observed in modern sloths, indicating that ground sloth juveniles may have engaged in similar behaviors to those of modern sloths, such as clinging to their mothers for transportation. Ground sloth juveniles also possess morphological traits that have been linked with semiarboreal behaviors.
DOI: 10.6084/m9.figshare.7957505
title: Stratigraphic architecture and hierarchy of fluvial overbank splay deposits

description: Primary field data: Thickness and facies types with GPS co-ordinates; Length and width vs thickness; Modern data and co-ordinates.
DOI: 10.6084/m9.figshare.7957355
title: Context-assignment-based-ABCmodel(FUS-TARDBP)

description: This is the results from Context-assignment-based-ABCmodel for FUS-TARDBP relation.Each file shows results according to similarity difference.
DOI: 10.6084/m9.figshare.7957355.v1
title: Context-assignment-based-ABCmodel(FUS-TARDBP)

description: This is the results from Context-assignment-based-ABCmodel for FUS-TARDBP relation.Each file shows results according to similarity difference.
DOI: 10.6084/m9.figshare.7957352
title: Supplementary Material for: Comparison of Solute Clearance, Hospitalization Rate, and Aortic Arch Calcification between Online Hemodiafiltration and High-Flux Hemodialysis: A 6-Year Observational Study

description: <b><i>Background/Aims:</i></b> Studies on the long-term clinical benefits of hemodiafiltration (HDF) and high-flux hemodialysis (HFHD) are very limited. This study aimed to investigate the hospitalization rate and aortic arch calcification (AAC) of these two dialysis modalities over 6 years. <b><i>Methods:</i></b> Participants who received regular HDF and HFHD in one hospital-facilitated hemodialysis center were prospectively enrolled after matching for age, sex, and diabetes between January 2009 and December 2014. Medical records were reviewed retrospectively on demographics, laboratory variables, calcified scores in aortic arch measured by chest radiography, and rates of hospital admission. Cox proportional hazard regression and linear regression were used to obtain the outcome results. <b><i>Results:</i></b> The HDF and HFHD groups consisted of 108 and 102 participants, respectively. Levels of laboratory variables including small soluble solutes and Kt/V were not statistically different over the 6-year period between the HDF and HFHD groups. Calcified scores of the aortic arch increased over 6 years in both groups. The changes in the mean calcified scores were significant when compared between the two groups (0.44–1.82 in HFHD, 0.79–1.8 in HDF, respectively, <i>p</i> = 0.008). Hospitalization rates were 735 per 1,000 patients in the HDF group and 852 per 1,000 patients in the HFHD group, respectively. No significant difference was observed in frequency and days of hospitalization between HDF and HFHD. <b><i>Conclusion:</i></b> Hospitalization rates and AAC were observed to be equal for HDF and HFHD.
DOI: 10.6084/m9.figshare.7957346
title: Context-based-ABCmodel(FUS-TARDBP)

description: This is the results from Context-based-ABCmodel for FUS-TARDBP relation.Each file shows results according to similarity difference.<br>
DOI: 10.6084/m9.figshare.7957349
title: Context-assignment-based ABC model (APOE-MAPT)

description: This is the results from Context-assignment-based-ABCmodel for APOE-MAPT relation.Each file shows results according to similarity difference.
DOI: 10.6084/m9.figshare.7957352.v1
title: Supplementary Material for: Comparison of Solute Clearance, Hospitalization Rate, and Aortic Arch Calcification between Online Hemodiafiltration and High-Flux Hemodialysis: A 6-Year Observational Study

description: <b><i>Background/Aims:</i></b> Studies on the long-term clinical benefits of hemodiafiltration (HDF) and high-flux hemodialysis (HFHD) are very limited. This study aimed to investigate the hospitalization rate and aortic arch calcification (AAC) of these two dialysis modalities over 6 years. <b><i>Methods:</i></b> Participants who received regular HDF and HFHD in one hospital-facilitated hemodialysis center were prospectively enrolled after matching for age, sex, and diabetes between January 2009 and December 2014. Medical records were reviewed retrospectively on demographics, laboratory variables, calcified scores in aortic arch measured by chest radiography, and rates of hospital admission. Cox proportional hazard regression and linear regression were used to obtain the outcome results. <b><i>Results:</i></b> The HDF and HFHD groups consisted of 108 and 102 participants, respectively. Levels of laboratory variables including small soluble solutes and Kt/V were not statistically different over the 6-year period between the HDF and HFHD groups. Calcified scores of the aortic arch increased over 6 years in both groups. The changes in the mean calcified scores were significant when compared between the two groups (0.44–1.82 in HFHD, 0.79–1.8 in HDF, respectively, <i>p</i> = 0.008). Hospitalization rates were 735 per 1,000 patients in the HDF group and 852 per 1,000 patients in the HFHD group, respectively. No significant difference was observed in frequency and days of hospitalization between HDF and HFHD. <b><i>Conclusion:</i></b> Hospitalization rates and AAC were observed to be equal for HDF and HFHD.
DOI: 10.6084/m9.figshare.7957349.v1
title: Context-assignment-based ABC model (APOE-MAPT)

description: This is the results from Context-assignment-based-ABCmodel for APOE-MAPT relation.Each file shows results according to similarity difference.
DOI: 10.6084/m9.figshare.7957340
title: Fuzzy ontology-based foreshore identification from digital terrain models and very high-resolution airborne imagery through GEOBIA multi-scale analysis

description: Coastal mapping provides information for coastal zone protection. Land foreshore-border mapping is important, since it is related to land and property management, raising the need for an automated foreshore delineation framework. This research develops a multi-scale GEographic Object-Based Image Analysis method for foreshore identification from single-date very high-resolution imagery and DTM. Foreshore interpretation criteria were provided by the Greek Cadastral Office; however, they defined the foreshore-borders in an ill-defined manner. Thus, an ontology was designed and implemented to formalize the implicit spectral, geometric, and spatial relationships described in the interpretation criteria, and employ them during identification. The final ontology was delivered after three design phases: specification, conceptualization, and knowledge formalization. Imagery preprocessing through anisotropic morphological levelings reduced undesired spatial detail and noise. A three-level segmentation and ontological classification approach was developed to compute proper objects and assign them into semantic categories. Class definitions were created through fuzzy restrictions, representing value ranges of the employed properties. Evaluation of the extracted foreshore area with human-interpreted reference data showed a 77.9% quality, which was satisfactory. Evaluation by comparing the extracted foreshore border to the reference data showed an average deviation of 2.4 m, which is within Greek Cadastral Office specifications.
DOI: 10.6084/m9.figshare.7957337
title: Supplementary Material for: Higher in vivo Cortical Intracellular Volume Fraction Associated with Lithium Therapy in Bipolar Disorder: A Multicenter NODDI Study

description: <b><i>Background:</i></b> MRI studies in patients with bipolar disorder have suggested that lithium is associated with grey matter increases that may underlie its therapeutic effects. However, the relationship between grey matter volume and cellular microstructural changes is not straightforward, as modifications of different cellular compartments of grey matter may be involved. <b><i>Objectives:</i></b> Our aim was to test the hypothesis that dendritic density is higher in patients undergoing lithium therapy than in patients without lithium, using advanced modelling of water diffusion investigated with MRI. <b><i>Method:</i></b> We included 41 patients and 40 controls matched for age and gender from two sites. All subjects underwent 3T MRI with 3 shells of diffusion. We used neurite orientation dispersion and density imaging to compare the grey matter neurite density between patients undergoing lithium therapy or not and control subjects. <b><i>Results:</i></b> We found a significant group effect in the left prefrontal region (<i>p</i> = 0.001, Bonferroni corrected): patients without lithium had a lower frontal neurite density than controls (<i>p</i> = 0.009), while those on lithium had a higher mean neurite density than those without (<i>p</i> &lt; 0.001). Patients on lithium were not different from controls (<i>p</i> = 0.08). <b><i>Conclusions:</i></b> This is the first study to report in vivo evidence of preserved neurite density of the prefrontal cortex in humans associated with lithium intake. Changes of intracellular volume fraction are thought to reflect changes of grey matter microstructural organization. This reinforces the hypothesis of lithium having a positive effect on the neuronal compartment in humans.
DOI: 10.6084/m9.figshare.7957340.v1
title: Fuzzy ontology-based foreshore identification from digital terrain models and very high-resolution airborne imagery through GEOBIA multi-scale analysis

description: Coastal mapping provides information for coastal zone protection. Land foreshore-border mapping is important, since it is related to land and property management, raising the need for an automated foreshore delineation framework. This research develops a multi-scale GEographic Object-Based Image Analysis method for foreshore identification from single-date very high-resolution imagery and DTM. Foreshore interpretation criteria were provided by the Greek Cadastral Office; however, they defined the foreshore-borders in an ill-defined manner. Thus, an ontology was designed and implemented to formalize the implicit spectral, geometric, and spatial relationships described in the interpretation criteria, and employ them during identification. The final ontology was delivered after three design phases: specification, conceptualization, and knowledge formalization. Imagery preprocessing through anisotropic morphological levelings reduced undesired spatial detail and noise. A three-level segmentation and ontological classification approach was developed to compute proper objects and assign them into semantic categories. Class definitions were created through fuzzy restrictions, representing value ranges of the employed properties. Evaluation of the extracted foreshore area with human-interpreted reference data showed a 77.9% quality, which was satisfactory. Evaluation by comparing the extracted foreshore border to the reference data showed an average deviation of 2.4 m, which is within Greek Cadastral Office specifications.
DOI: 10.6084/m9.figshare.7957319
title: Context_based_ABCmodel(APOE_MAPT)

description: This is the results from Context-based-ABCmodel for APOE_MAPT relation.Each file shows results according to similarity difference.<br><br>
DOI: 10.6084/m9.figshare.7957337.v1
title: Supplementary Material for: Higher in vivo Cortical Intracellular Volume Fraction Associated with Lithium Therapy in Bipolar Disorder: A Multicenter NODDI Study

description: <b><i>Background:</i></b> MRI studies in patients with bipolar disorder have suggested that lithium is associated with grey matter increases that may underlie its therapeutic effects. However, the relationship between grey matter volume and cellular microstructural changes is not straightforward, as modifications of different cellular compartments of grey matter may be involved. <b><i>Objectives:</i></b> Our aim was to test the hypothesis that dendritic density is higher in patients undergoing lithium therapy than in patients without lithium, using advanced modelling of water diffusion investigated with MRI. <b><i>Method:</i></b> We included 41 patients and 40 controls matched for age and gender from two sites. All subjects underwent 3T MRI with 3 shells of diffusion. We used neurite orientation dispersion and density imaging to compare the grey matter neurite density between patients undergoing lithium therapy or not and control subjects. <b><i>Results:</i></b> We found a significant group effect in the left prefrontal region (<i>p</i> = 0.001, Bonferroni corrected): patients without lithium had a lower frontal neurite density than controls (<i>p</i> = 0.009), while those on lithium had a higher mean neurite density than those without (<i>p</i> &lt; 0.001). Patients on lithium were not different from controls (<i>p</i> = 0.08). <b><i>Conclusions:</i></b> This is the first study to report in vivo evidence of preserved neurite density of the prefrontal cortex in humans associated with lithium intake. Changes of intracellular volume fraction are thought to reflect changes of grey matter microstructural organization. This reinforces the hypothesis of lithium having a positive effect on the neuronal compartment in humans.
DOI: 10.6084/m9.figshare.7957319.v1
title: Context_based_ABCmodel(APOE_MAPT)

description: This is the results from Context-based-ABCmodel for APOE_MAPT relation.Each file shows results according to similarity difference.<br><br>
DOI: 10.5281/zenodo.4000342
title: CROCCA-2S Perth Canyon Multibeam Survey (The squirrel survey)

description: Multi-beam survey of Perth Canyon (on board the R/V Thomas Thompson) as part of the Coring to Reconstruct Ocean Circulation and Carbon Dioxide Across 2 Seas (CROCCA-2S) research cruise.