cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4793992.v1
title: Malignancies in transplanted patients: Multidisciplinary evaluation and switch to mTOR inhibitors after kidney transplantation – experiences from a prospective, clinical, observational study

description: <b>Background</b> Solid organ transplant recipients are at increased risk of developing malignancies. The objective of this prospective, observational, one-armed study was to study the feasibility to add a mammalian target of rapamycin (mTOR) inhibitor to the immunosuppressive regimen in transplanted patients with post-transplant malignancies. During the trial the need to improve identification of post-transplant malignancies and to reassure adequate oncological treatment of these patients became evident. Multidisciplinary team (MDT) evaluation of oncological and immunosuppressive treatments was implemented for all patients with malignancies after renal or combined renal and pancreas transplantation because of the trial. <b>Material and methods</b> At Uppsala University Hospital, Sweden, a MDT consisting of transplant surgeons, nephrologists, oncologists and dermatologists evaluated 120 renal or combined renal and pancreas-transplanted recipients diagnosed with malignancies from September 2006 to July 2012. To identify all malignancies, the population was linked to the Regional Tumor Registry (RTR). We recorded to which extent a switch to mTOR inhibitors was possible and how often the originally planned oncological managements were adjusted. All patients were followed for three years. (ClinicalTrials.gov: NCT02241564). <b>Results</b> In 76 of 120 patients (63%) a switch to mTOR inhibitors was possible. Immunosuppression was interrupted in seven patients (6%), reduced in three patients (2%) and remained unchanged in 34 of 120 patients (28%). Identification of post-transplant malignancies increased significantly after linkage to RTR (<i>p</i> = 0.015). The initially recommended oncological treatment was adjusted in 23 of 44 patients (52%) with solid or hematological malignancies; 36 of these patients (82%) were treated according to national guidelines. <b>Conclusion</b> In two thirds of the patients the immunosuppressive treatment could be changed to an mTOR inhibitor with anti-tumor effects in transplanted patients with post-transplant malignancies. The use of regional tumor registers considerably improved the identification of patients with post-transplant malignancies indicating that post-transplant malignancies might be timely underreported in transplant registers.
DOI: 10.6084/m9.figshare.4796548.v3
title: Which types of research are newsworthy? UK newspapers 2006-2015 citing Web of Science journals

description: Citations from news stories to scientific journals provide useful evidence about the dissemination of research findings to the public. This paper introduces a citation-based method to obtain information about news coverage of research on a large scale. ProQuest was used to search for citations to 9,639 Science and 3,412 Social Science Web of Science (WoS) journals from eight UK daily newspapers during 2006-2015 and an automatic method was applied to extract citations to academic journals from the full text of newspapers. Most Science (95%) and Social Science (94%) journals were never cited by these newspapers. Half of the cited Science journals covered medical or health-related topics, whereas 43% of the Social Sciences journals were related to psychiatry or psychology. A content analysis of the citing news stories found that the method identifies mentions of journals in news stories with very high accuracy and 94% of the journals mentioned reported research findings. From the citing news stories, 60% described research extensively and 53% used more than one source. There were variations in the extent to which newspapers reported good or bad news and most news stories had no comments about the quality of the reported research. Finally, a small number of prestigious British journals were cited often.
DOI: 10.6084/m9.figshare.4793905
title: Phytoplankton ecology of a culturally eutrophic embayment: Hamilton Harbour, Lake Ontario

description: Hamilton Harbour is a chronically eutrophic embayment located at the western end of Lake Ontario that has experienced many decades of agricultural, industrial, and urban contamination. It has been identified as an Area of Concern under the terms of the Great Lakes Water Quality Agreement between Canada and the United States. This study examines the ecology of the phytoplankton communities at one centrally located station during the ice-free period (May–October) of three non-consecutive years: 2002, 2004 and 2006. This was the first comprehensive study to be conducted since the 1970s. It was found that the phytoplankton communities are diverse and fluctuate throughout the year, along with changing nutrient, physical and environmental conditions. No consistent patterns of seasonal succession were observed throughout the study. Phytoflagellates including Cryptophyceae and Dinophyceae had a tendency to outnumber and out-compete other phytoplankton since they are mobile and able to seek out optimal habitats within the water column. For a highly eutrophic water body, algal biomass (annual mean ≈ 2.0 g m<sup>−3</sup>) was lower than expected and more consistent with mesotrophic conditions–an observation first made by researchers in the 1970s and attributed to the highly variable physical environment. While our study supports these earlier results, we also conclude that zooplankton grazing likely has a significant role in limiting the size of the algal standing crop. Several algal bloom events were captured during our study. In addition to the somewhat predictable blooms of Diatomeae in the spring and Cyanophyta in the summer, we also observed blooms of Cryptophyceae and Dinophyceae. In one case we observed a bloom with no dominant taxon–it contained a diverse mixture of Cryptophyceae, Euglenophyta and Dinophyceae–challenging the commonly held notion that algal blooms are essentially monocultures. Our results show that such a variable and stressed ecosystem requires frequent sampling to capture the rapid changes that occur.
DOI: 10.6084/m9.figshare.4793896
title: 1MiB.dat

description: Test2
DOI: 10.6084/m9.figshare.4793905.v2
title: Phytoplankton ecology of a culturally eutrophic embayment: Hamilton Harbour, Lake Ontario

description: Hamilton Harbour is a chronically eutrophic embayment located at the western end of Lake Ontario that has experienced many decades of agricultural, industrial, and urban contamination. It has been identified as an Area of Concern under the terms of the Great Lakes Water Quality Agreement between Canada and the United States. This study examines the ecology of the phytoplankton communities at one centrally located station during the ice-free period (May–October) of three non-consecutive years: 2002, 2004 and 2006. This was the first comprehensive study to be conducted since the 1970s. It was found that the phytoplankton communities are diverse and fluctuate throughout the year, along with changing nutrient, physical and environmental conditions. No consistent patterns of seasonal succession were observed throughout the study. Phytoflagellates including Cryptophyceae and Dinophyceae had a tendency to outnumber and out-compete other phytoplankton since they are mobile and able to seek out optimal habitats within the water column. For a highly eutrophic water body, algal biomass (annual mean ≈ 2.0 g m<sup>−3</sup>) was lower than expected and more consistent with mesotrophic conditions–an observation first made by researchers in the 1970s and attributed to the highly variable physical environment. While our study supports these earlier results, we also conclude that zooplankton grazing likely has a significant role in limiting the size of the algal standing crop. Several algal bloom events were captured during our study. In addition to the somewhat predictable blooms of Diatomeae in the spring and Cyanophyta in the summer, we also observed blooms of Cryptophyceae and Dinophyceae. In one case we observed a bloom with no dominant taxon–it contained a diverse mixture of Cryptophyceae, Euglenophyta and Dinophyceae–challenging the commonly held notion that algal blooms are essentially monocultures. Our results show that such a variable and stressed ecosystem requires frequent sampling to capture the rapid changes that occur.
DOI: 10.6084/m9.figshare.4793905.v1
title: Phytoplankton ecology of a culturally eutrophic embayment: Hamilton Harbour, Lake Ontario

description: Hamilton Harbour is a chronically eutrophic embayment located at the western end of Lake Ontario that has experienced many decades of agricultural, industrial, and urban contamination. It has been identified as an Area of Concern under the terms of the Great Lakes Water Quality Agreement between Canada and the United States. This study examines the ecology of the phytoplankton communities at one centrally located station during the ice-free period (May-October) of three non-consecutive years: 2002, 2004 and 2006. This was the first comprehensive study to be conducted since the 1970s. It was found that the phytoplankton communities are diverse and fluctuate throughout the year, along with changing nutrient, physical and environmental conditions. No consistent patterns of seasonal succession were observed throughout the study. Phytoflagellates including Cryptophyceae and Dinophyceae had a tendency to outnumber and out-compete other phytoplankton since they are mobile and able to seek out optimal habitats within the water column. For a highly eutrophic water body, algal biomass (annual mean ≈ 2.0 g m<sup>-3</sup>) was lower than expected and more consistent with mesotrophic conditions – an observation first made by researchers in the 1970s and attributed to the highly variable physical environment. While our study supports these earlier results, we also conclude that zooplankton grazing likely has a significant role in limiting the size of the algal standing crop. Several algal bloom events were captured during our study. In addition to the somewhat predictable blooms of Diatomeae in the spring and Cyanophyta in the summer, we also observed blooms of Cryptophyceae and Diatomeae. In one case we observed a bloom with no dominant taxon – it contained a diverse mixture of Cryptophyceae, Euglenophyta and Dinophyceae – challenging the commonly held notion that algal blooms are essentially monocultures. Our results show that such a variable and stressed ecosystem requires frequent sampling to capture the rapid changes that occur.
DOI: 10.6084/m9.figshare.4793896.v2
title: 1MiB.dat

description: Test2
DOI: 10.6084/m9.figshare.4793896.v1
title: 1MiB.dat

description: Test2
DOI: 10.6084/m9.figshare.4793818
title: AtSLP2 is an intronless protein phosphatase that co-expresses with intronless mitochondrial pentatricopeptide repeat (PPR) and tetratricopeptide (TPR) protein encoding genes

description: Shewanella-like PPP family phosphatases (SLPs) are a unique lineage of eukaryote PPP-family phosphatases of bacterial origin which are not found in metazoans.<sup>1,2</sup> Their absence in metazoans is marked by their ancient bacterial origins and presence in plants.<sup>1</sup> Recently, we found that the SLP2 phosphatase ortholog of Arabidopsis thaliana localized to the mitochondrial intermembrane space (IMS) where it was determined to be activated by mitochondrial intermembrane space protein 40 (MIA40) to regulate seed germination.<sup>3</sup> Through examination of <i>atslp2</i> knockout (accelerated germination) and 35S::AtSLP2 over-expressing (delayed germination) plants it was found that AtSLP2 influences <i>Arabidopsis thaliana</i> germination rates via gibberellic acid (GA) biosynthesis.<sup>3</sup> However, the exact mechanism by which this occurs remains unresolved. To identify potential partners of AtSLP2 in regulating germination through GA, we undertook a gene co-expression network analysis using RNA-sequencing data available through Genevestigator (https://genevestigator.com/gv/).
DOI: 10.6084/m9.figshare.4793818.v1
title: AtSLP2 is an intronless protein phosphatase that co-expresses with intronless mitochondrial pentatricopeptide repeat (PPR) and tetratricopeptide (TPR) protein encoding genes

description: Shewanella-like PPP family phosphatases (SLPs) are a unique lineage of eukaryote PPP-family phosphatases of bacterial origin which are not found in metazoans.<sup>1,2</sup> Their absence in metazoans is marked by their ancient bacterial origins and presence in plants.<sup>1</sup> Recently, we found that the SLP2 phosphatase ortholog of Arabidopsis thaliana localized to the mitochondrial intermembrane space (IMS) where it was determined to be activated by mitochondrial intermembrane space protein 40 (MIA40) to regulate seed germination.<sup>3</sup> Through examination of <i>atslp2</i> knockout (accelerated germination) and 35S::AtSLP2 over-expressing (delayed germination) plants it was found that AtSLP2 influences <i>Arabidopsis thaliana</i> germination rates via gibberellic acid (GA) biosynthesis.<sup>3</sup> However, the exact mechanism by which this occurs remains unresolved. To identify potential partners of AtSLP2 in regulating germination through GA, we undertook a gene co-expression network analysis using RNA-sequencing data available through Genevestigator (https://genevestigator.com/gv/).
DOI: 10.6084/m9.figshare.4793773
title: Supplementary Material for: Clinical and Dermoscopic Features of the Scalp in 31 Patients with Dermatomyositis

description: <b><i>Background:</i></b> Scalp involvement is not directly evaluated in patients with dermatomyositis (DM). Therefore, the exact frequency of scalp dermatomyositis (SDM) and its clinical and trichoscopic characteristics have been poorly described. <b><i>Objective:</i></b> The aim of this study was to determine the frequency and clinical and dermoscopic features of SDM in patients diagnosed with DM. <b><i>Methods:</i></b> We performed a descriptive prospective, cross-sectional observational study that included all patients diagnosed with DM at a Mexican academic institute over the course of a year. <b><i>Results:</i></b> Twenty-four out of 31 patients with DM had scalp involvement at clinical examination, with a prevalence of 77.4%. SDM was clinically characterized by erythema in all cases, scales in 20 (83.3%) patients, nonscarring alopecia in 21 (87.5%) patients, pruritus in 17 (70.8%) patients, and poikiloderma of the scalp in 16 (51.6%) patients. Twenty-eight patients were evaluated by trichoscopy. The most consistent finding was the presence of enlarged capillaries, found in 20 (71.4%) cases, followed by peripilar casts (57.1%) and tufting and interfollicular scales in 14 (50%) cases. Twenty-two patients also had positive nail fold capillaroscopic features similar to those observed by trichoscopy. <b><i>Limitations:</i></b> The simple size was limited. <b><i>Conclusions:</i></b> Scalp involvement and alopecia are common in patients with DM, and trichoscopy shows features similar to those found at capillaroscopy. Trichoscopy is a very important tool for diagnosis of scalp involvement in patients with DM.
DOI: 10.6084/m9.figshare.4793761
title: ANVIO-FMT-DONOR-MAGs-IN-HMP-METAGENOMES

description: Individual anvi'o profiles for the occurrence of each the FMT donor MAG across 151 HMP gut metagenomes.
DOI: 10.6084/m9.figshare.4793737
title: Supplementary Material for: Genome-Wide Identification and Analysis of the Type-B Authentic Response Regulator Gene Family in Peach (Prunus persica)

description: The type-B authentic response regulator (ARR-B) family members serve as DNA-binding transcriptional regulators, whose activities are probably regulated by phosphorylation/dephosphorylation, resulting in the rapid induction of type-A ARR genes. Type-B ARRs are believed to be involved in many biological processes, including cytokinin signaling, plant growth, and stress responses through a chaperone or by isomerization of proline residues during protein folding. The public availability of complete peach genome sequences allows the identification of 23 ARR-B genes by HMMER and blast analysis. Scaffold locations of these genes in the peach genome were determined, and the protein domain and motif organization of peach type-B ARRs were analyzed. The phylogenetic relationships between peach type-B ARRs were also assessed. The expression profiles of peach ARR-B genes revealed that most of the type-B ARRs showed high expression levels in tissues undergoing rapid cell division and may engage more cytokinins, like half-opened flowers, fruits at expansion stages, and young leaves. These findings not only contribute to a better understanding of the complex regulation of the peach ARR-B gene family, but also provide valuable information for future research in peach functional genomics.
DOI: 10.6084/m9.figshare.4793734
title: Sexual signals reflect telomere dynamics in a wild bird

description: This is the data and code supporting the following publication:<br>Taff, C.C., & Freeman-Gallant, C.R. 2017. Sexual signals reflect telomere dynamics in a wild bird. Ecology & Evolution. http://doi.org/10.1002/ece3.2948<br>See annotation in R script for notes and explanation of data and analysis included.
DOI: 10.6084/m9.figshare.4793758
title: Supplementary Material for: A Comparison of Different Training Methods in the Successful Learning of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration

description: <b><i>Background:</i></b> Standardized training of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS- TBNA) is available only in highly developed countries. <b><i>Objective:</i></b> To compare the skill differences in the performance of EBUS-TBNA by pulmonologists trained under different learning methods. <b><i>Methods:</i></b> We performed a retrospective study of 145 EBUS-TBNA cases. We set up 3 comparative training groups: a standardized training group, a teaching group, and a self-study group. The main clinical outcomes were sensitivity, specificity and accuracy of EBUS-TBNA. Cumulative sum analysis was used to track EBUS-TBNA proficiency of the 3 groups. <b><i>Results:</i></b> The sensitivities of EBUS-TBNA in the different groups were 90, 88, and 67%, respectively. The accuracies of the different groups were 91, 90, and 71%, respectively. With respect to the sensitivity and accuracy, there was no significant difference between the standardized training group and teaching group. However, the self-study group was inferior to the other 2 groups. By comparing the learning curve among the groups, we found that the minimum number of operations needed to reach a 90% accuracy for the standardized training group, the teaching group and the self-study group was 17, 32 and 40 cases, respectively. <b><i>Conclusion:</i></b> Compared with the teaching and self-study groups, the standardized training group resulted in practitioners achieving high skill levels following the performance of a lower number of cases. Pulmonologists trained in the teaching group achieved a similar level of skills, but required more experience to reach this level. Practitioners in the self-study group did not achieve a satisfactory level of skills, despite performing a high number of cases.
DOI: 10.6084/m9.figshare.4793722
title: Supplementary Material for: Influence of Feeding Types during the First Months of Life on Calciuria Levels in Healthy Infants: A Secondary Analysis from a Randomized Clinical Trial

description: <b><i>Background/Aims:</i></b> Dietary factors can modify calciuria. We aim to investigate urinary calcium excretion in healthy infants according to their protein. <b><i>Methods:</i></b> Secondary data analysis from a randomized clinical trial where healthy term infants were randomized after birth to a higher (HP) or lower (LP) protein content formula that was consumed until age 1 year. A non-randomized group of breastfed (BF) infants was used for reference. Anthropometry, dietary intakes and calciuria (calcium/creatinine ratios) from spot urine samples were assessed at ages 3 and 6 months. At 6 months, the kidney volumes were assessed using ultrasonography, and the serum urea and creatinine levels were determined. <b><i>Results:</i></b> BF infants showed the highest calciuria levels, followed by the HP and the LP groups (<i>p</i> &lt; 0.001 for all comparisons). Either protein intakes or formula types modulated the calciuria in linear regression models adjusted for other influencing dietary factors. The usual cut-off values classified 37.8% (BF), 16.8% (HP) and 4.9% (LP) of the infants as hypercalciuric. <b><i>Conclusions:</i></b> Feeding types during the first months of life affect calciuria, with BF infants presenting the highest levels. We propose new cut-off values, based on feeding types, to prevent the overestimation in hypercalciuria diagnoses among BF infants.
DOI: 10.6084/m9.figshare.4793734.v1
title: Sexual signals reflect telomere dynamics in a wild bird

description: This is the data and code supporting the following publication:<br>Taff, C.C., & Freeman-Gallant, C.R. 2017. Sexual signals reflect telomere dynamics in a wild bird. Ecology & Evolution. http://doi.org/10.1002/ece3.2948<br>See annotation in R script for notes and explanation of data and analysis included.
DOI: 10.6084/m9.figshare.4793758.v1
title: Supplementary Material for: A Comparison of Different Training Methods in the Successful Learning of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration

description: <b><i>Background:</i></b> Standardized training of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS- TBNA) is available only in highly developed countries. <b><i>Objective:</i></b> To compare the skill differences in the performance of EBUS-TBNA by pulmonologists trained under different learning methods. <b><i>Methods:</i></b> We performed a retrospective study of 145 EBUS-TBNA cases. We set up 3 comparative training groups: a standardized training group, a teaching group, and a self-study group. The main clinical outcomes were sensitivity, specificity and accuracy of EBUS-TBNA. Cumulative sum analysis was used to track EBUS-TBNA proficiency of the 3 groups. <b><i>Results:</i></b> The sensitivities of EBUS-TBNA in the different groups were 90, 88, and 67%, respectively. The accuracies of the different groups were 91, 90, and 71%, respectively. With respect to the sensitivity and accuracy, there was no significant difference between the standardized training group and teaching group. However, the self-study group was inferior to the other 2 groups. By comparing the learning curve among the groups, we found that the minimum number of operations needed to reach a 90% accuracy for the standardized training group, the teaching group and the self-study group was 17, 32 and 40 cases, respectively. <b><i>Conclusion:</i></b> Compared with the teaching and self-study groups, the standardized training group resulted in practitioners achieving high skill levels following the performance of a lower number of cases. Pulmonologists trained in the teaching group achieved a similar level of skills, but required more experience to reach this level. Practitioners in the self-study group did not achieve a satisfactory level of skills, despite performing a high number of cases.