cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5126395
title: Supplementary Material for: Infrastructure and Facilities for Human Biobanking in Low- and Middle-Income Countries: A Situation Analysis

description: <b><i>Objective:</i></b> To collect information on biobanking facilities in low- and middle-income countries (LMICs) as a first step towards establishing an LMIC biobank and cohort building network (BCNet) to support research, with a focus on cancer control. <b><i>Method:</i></b> Sixty centres were identified from sources including cancer centres, universities, hospitals, and public health facilities and invited to participate in a survey between December 2012 and March 2013. <b><i>Results:</i></b> Of the 27 centres (45%) that responded, most have existed for &lt;10 years. They store between 1,000 and 1,000,000 research samples as well as samples remaining after clinical diagnosis. Sample storage is mostly in freezers, although 45% (9/20) of the centres do not have regular access to electricity. Biobank managers, sample management systems, and mechanisms for follow-up using linkages are uncommon. Many (80%; 21/26) of the centres have regulations to govern research, but regulations for the use of biobank resources (samples and data) are not well developed. <b><i>Conclusions:</i></b> Biobanking facilities are being developed in LMICs. Shortcomings in international visibility, sample sharing regulations, standardization, quality assurance, and sample management systems could be alleviated by international networking. Stakeholders need to work together to increase access to high-quality biological resources for scientific research.
DOI: 10.6084/m9.figshare.5126398.v1
title: Supplementary Material for: Effects of Crit-Line® Monitor Use on Patient Outcomes and Epoetin Alfa Dosing following Onset of Hemodialysis: A Propensity Score-Matched Study

description: <b><i>Background:</i></b> The Crit-Line® monitor (CLM) is a device for monitoring hematocrit, oxygen saturation and change in intravascular blood volume during hemodialysis. Prior studies have evaluated CLM use in dialysis patients, but not specifically in those new to dialysis. <b><i>Methods:</i></b> In this retrospective analysis, 199 patients initiating dialysis at 8 facilities routinely using CLM were compared with 796 propensity score-matched non-CLM patients initiating dialysis at facilities not using CLM. Outcomes were considered over the first 180 days on dialysis. <b><i>Results:</i></b> Overall, the CLM group had higher StdKt/V (p = 0.06) and received lower doses of intravenous iron than the non-CLM group (p &lt; 0.001). Erythropoiesis-stimulating agent doses were lower in the CLM group in months 1-5. Serum iron and transferrin saturation levels were higher overall for the CLM group than the non-CLM group (p = 0.004 and 0.01, respectively). Hemoglobin levels and time to first hospitalization were similar for both groups. <b><i>Conclusion:</i></b> Use of CLM is associated with lower erythropoiesis-stimulating agent and iron use in incident hemodialysis patients.
DOI: 10.6084/m9.figshare.5126386
title: Supplementary Material for: Uterine Artery Pulsatility Index Assessment at 11-13<sup>+6</sup> Weeks' Gestation

description: <b><i>Introduction:</i></b> First-trimester uterine artery pulsatility index (PI) measurements form part of an algorithm used to assess the risk of developing pre-eclampsia. The objective of this study was to construct a population-specific reference range for both the lower and mean maternal uterine artery PI at 11-13<sup>+6</sup> weeks' gestation and to assess measurement agreement. <b><i>Materials and Methods:</i></b> Reference ranges for mean and lower PI measurements were developed using polynomial regression models following prospective collection of maternal uterine artery PI measurements at 11-13<sup>+6</sup> weeks' gestation. Measurement agreement studies were performed by two experienced operators. <b><i>Results:</i></b> Measurements from 298 women were included in the primary study. Polynomial regression indicated no change over gestational age for the lower PI (mean 1.44). There was an inverse relationship between the average PI and gestational age (mean [0.8960 + (2.9771 × CRL<sup>-1/2</sup>)]<sup>2</sup>). PI measurement agreement was good-strong (intraclass correlation (ICC) 0.50-0.79) between operators, and within-operator agreement was almost perfect (ICC 0.88-0.93). <b><i>Conclusions:</i></b> Reference ranges for both the average and lowest PI of the maternal uterine arteries were derived at 11-13<sup>+6</sup> weeks' gestation. This will provide a basis for development of auditable standards for first-trimester uterine artery Doppler measurements. The PI measurements are reproducible and reliable.
DOI: 10.6084/m9.figshare.5126383
title: Supplementary Material for: Fetal Bronchoscopy as a Useful Procedure in a Case with Prenatal Diagnosis of Congenital Microcystic Adenomatoid Malformation

description: Massive microcystic congenital cystic adenomatoid malformation (CCAM) and bronchial atresia are associated with a high perinatal mortality secondary to lung hypoplasia and cardiac dysfunction, and fetal intervention should be considered to improve prognosis. Therapeutic options include open fetal surgery with pulmonary resection, fetal sclerotherapy and fetoscopy. We present a case with a severely enlarged left lung without ultrasound signs of dilated airways compatible with the diagnosis of microcystic CCAM, hydrops and severe contralateral lung hypoplasia that was treated successfully at 30 weeks of gestation by fetal bronchoscopy, through which bronchial atresia was identified at the end of the left mainstem bronchi and permeabilized by laser ablation. After fetal surgery, weekly follow-up showed a progressive decrease in the affected lung size and an increase in the contralateral hypoplastic lung size, demonstrating normal dimensions of both lungs at 34 weeks of gestation, reversal of the mediastinal shift, and complete disappearance of hydrops. A healthy neonate was delivered uneventfully at term with no need for respiratory support, and the boy is now doing well at 15 months of age. This report demonstrates that in cases with prenatal diagnosis of large microcystic CCAM, fetal bronchoscopy can be used to refine the diagnosis of bronchial atresia and as a therapeutic tool with good outcome.
DOI: 10.6084/m9.figshare.5126386.v1
title: Supplementary Material for: Uterine Artery Pulsatility Index Assessment at 11-13<sup>+6</sup> Weeks' Gestation

description: <b><i>Introduction:</i></b> First-trimester uterine artery pulsatility index (PI) measurements form part of an algorithm used to assess the risk of developing pre-eclampsia. The objective of this study was to construct a population-specific reference range for both the lower and mean maternal uterine artery PI at 11-13<sup>+6</sup> weeks' gestation and to assess measurement agreement. <b><i>Materials and Methods:</i></b> Reference ranges for mean and lower PI measurements were developed using polynomial regression models following prospective collection of maternal uterine artery PI measurements at 11-13<sup>+6</sup> weeks' gestation. Measurement agreement studies were performed by two experienced operators. <b><i>Results:</i></b> Measurements from 298 women were included in the primary study. Polynomial regression indicated no change over gestational age for the lower PI (mean 1.44). There was an inverse relationship between the average PI and gestational age (mean [0.8960 + (2.9771 × CRL<sup>-1/2</sup>)]<sup>2</sup>). PI measurement agreement was good-strong (intraclass correlation (ICC) 0.50-0.79) between operators, and within-operator agreement was almost perfect (ICC 0.88-0.93). <b><i>Conclusions:</i></b> Reference ranges for both the average and lowest PI of the maternal uterine arteries were derived at 11-13<sup>+6</sup> weeks' gestation. This will provide a basis for development of auditable standards for first-trimester uterine artery Doppler measurements. The PI measurements are reproducible and reliable.
DOI: 10.6084/m9.figshare.5126377
title: Supplementary Material for: Calcitonin Gene-Related Peptide Modulates the Production of Pro-Inflammatory Cytokines Associated with Periprosthetic Osteolysis by THP-1 Macrophage-Like Cells

description: <b><i>Objective:</i></b> An anti-resorptive impact of the neuropeptide calcitonin gene-related peptide (CGRP) on periprosthetic osteolysis, the leading cause of early prosthesis loosening, has been shown previously. In this study, the impact of CGRP on pro-inflammatory cytokine production associated with periprosthetic osteolysis was analysed using THP-1 macrophage-like cells. <b><i>Methods:</i></b> Cells were stimulated with ultra-high-molecular-weight polyethylene (UHMWPE) particles (cell-to-particle ratios of 1:100 and 1:500) and lipopolysaccharides (LPS; 1 µg/ml) to establish osteolytic conditions, and simultaneously treated with CGRP (10<sup>-8</sup>M). Receptor activator of nuclear factor-κB <i>(RANK)</i>, RANK ligand <i>(RANKL)</i> and tumour necrosis factor <i>(TNF)</i>-<i>a</i> mRNA expression were measured by quantitative RT-PCR. RANK protein was detected by Western blot. Secreted protein levels of TNF-a as well as interleukin (IL)-1ß and IL-6 were quantified in cell culture supernatants by ELISA and Bio-Plex cytokine assay, respectively. <b><i>Results:</i></b> Activation of macrophage-like cells failed to enhance the production of RANK but led to a dose- and time-dependent increase of <i>TNF</i>-<i>a</i> mRNA and secreted protein levels of TNF-a, IL-1ß and IL-6. Application of CGRP time-dependently suppressed <i>TNF-a</i> mRNA expression induced by low-particle concentrations and LPS, while both particle- and LPS-induced secretion of TNF-a was inhibited. A pronounced inhibitory effect of CGRP on LPS-induced cytokine production at 24 h of incubation was also observed with IL-1ß and IL-6. <b><i>Conclusions:</i></b> CGRP shows a time-dependent inhibitory effect on the secretion of osteolysis-associated pro-inflammatory cytokines, indicating an indirect anti-resorptive influence of the neuropeptide on both aseptic prosthesis loosening and bacterially induced bone resorption which might enhance the life time of total joint replacements.
DOI: 10.6084/m9.figshare.5126380
title: Supplementary Material for: Polyploidy and Hybridization as Main Factors of Speciation: Complex Reticulate Evolution within the Grass Genus <b><i>Helictochloa</i></b>

description: To study the origin and evolution of naturally occurring polyploids, we performed phylogenetic analyses of nuclear ribosomal DNA spacers combined with molecular cytogenetics in 55 accessions of 27 taxa of the oat genus <i>Helictochloa</i>. A complex pattern of reticulate evolution was revealed with many diploid species and extensive polyploidy up to 20x. Altogether 11 groups of internal transcribed spacer (ITS) sequences can be distinguished. Sequences from 1-3 different ITS lineages were detected in polyploids. Cytogenetic data allow reconstruction of 8 basic monoploid chromosome sets. Six of these genomes occur in different combinations in the polyploid species. Two genomes are only found in diploids. Our sequence and karyological data highlight the occurrence of autopolyploidy and allopolyploidy, provide new information about the evolutionary history of taxa, and allow a more accurate systematic treatment of the concerned species. The geographical distribution of the 11 ITS lineages distinguished is highly structured and points to an origin of the genus in western Asia, presumably in grasslands like steppes or mountain steppes and meadows. The evolutionary basal lineages are of Asian, Minor Asian and east Mediterranean distribution and are present also in North America. The western and central parts of the Mediterranean and northern Europe harbor the modern lineages.
DOI: 10.6084/m9.figshare.5126383.v1
title: Supplementary Material for: Fetal Bronchoscopy as a Useful Procedure in a Case with Prenatal Diagnosis of Congenital Microcystic Adenomatoid Malformation

description: Massive microcystic congenital cystic adenomatoid malformation (CCAM) and bronchial atresia are associated with a high perinatal mortality secondary to lung hypoplasia and cardiac dysfunction, and fetal intervention should be considered to improve prognosis. Therapeutic options include open fetal surgery with pulmonary resection, fetal sclerotherapy and fetoscopy. We present a case with a severely enlarged left lung without ultrasound signs of dilated airways compatible with the diagnosis of microcystic CCAM, hydrops and severe contralateral lung hypoplasia that was treated successfully at 30 weeks of gestation by fetal bronchoscopy, through which bronchial atresia was identified at the end of the left mainstem bronchi and permeabilized by laser ablation. After fetal surgery, weekly follow-up showed a progressive decrease in the affected lung size and an increase in the contralateral hypoplastic lung size, demonstrating normal dimensions of both lungs at 34 weeks of gestation, reversal of the mediastinal shift, and complete disappearance of hydrops. A healthy neonate was delivered uneventfully at term with no need for respiratory support, and the boy is now doing well at 15 months of age. This report demonstrates that in cases with prenatal diagnosis of large microcystic CCAM, fetal bronchoscopy can be used to refine the diagnosis of bronchial atresia and as a therapeutic tool with good outcome.
DOI: 10.6084/m9.figshare.5126368
title: Supplementary Material for: Prestroke Physical Activity Is Associated with Good Functional Outcome and Arterial Recanalization after Stroke due to a Large Vessel Occlusion

description: <b><i>Background:</i></b> Although multiple studies and meta-analyses have consistently suggested that regular physical activity (PhA) is associated with a decreased stroke risk and recurrence, there is limited data on the possible preconditioning effect of prestroke PhA on stroke severity and prognosis. We aimed to study the association of prestroke PhA with different outcome variables in patients with acute ischemic stroke due to an anterior large vessel occlusion. <b><i>Methods:</i></b> The Prestroke Physical Activity and Functional Recovery in Patients with Ischemic Stroke and Arterial Occlusion trial is an observational and longitudinal study that included consecutive patients with acute ischemic stroke admitted to a single tertiary stroke center. Main inclusion criteria were: anterior circulation ischemic stroke within 12 h from symptom onset; presence of a confirmed anterior large vessel occlusion, and functional independence previous to stroke. Prestroke PhA was evaluated with the International Physical Activity Questionnaire and categorized into mild, moderate and high levels by means of metabolic equivalent (MET) minutes per week thresholds. The primary outcome measure was good functional outcome at 3 months (modified Rankin scale ≤2). Secondary outcomes were severity of stroke at admission, complete early recanalization, early dramatic neurological improvement and final infarct volume. <b><i>Results:</i></b> During the study period, 159 patients fulfilled the above criteria. The mean age was 68 years, 62% were men and the baseline NIHSS score was 17. Patients with high levels of prestroke PhA were younger, had more frequently distal occlusions and had lower levels of blood glucose and fibrinogen at admission. After multivariate analysis, a high level of prestroke PhA was associated with a good functional outcome at 3 months. Regarding secondary outcome variables and after adjustment for relevant factors, a high level of prestroke PhA was independently associated with milder stroke severity at admission, early dramatic improvement, early arterial recanalization after intravenous thrombolysis and lower final infarct volume. The beneficial association of prestroke PhA with stroke outcomes was already present with a cutoff point of 1,000 MET min/week, a level of PhA easily achieved by walking 1 h/day during 5 days or by doing a vigorous aerobic activity 1 h/day twice a week. <b><i>Conclusions:</i></b> Prestroke PhA is independently associated with favorable stroke outcomes after a large vessel occlusion. Future research on the underlying mechanisms is needed to understand this neuroprotective effect of PhA.
DOI: 10.6084/m9.figshare.5126371
title: Supplementary Material for: Infantile Hemangioma-Like Vascular Lesion in a 26-Year-Old Woman after Abortion

description: A 26-year-old woman (G2P1A1) presented with a 5-week history of multiple red marks on her body after a therapeutic abortion. A physical examination found 15 palpable red marks on her head, neck, chest, arms and legs. Proliferating endothelial cells, which expressed CD31, CD34, von Willebrand factor, but not Glut-1 and merosin, were observed in the lesional area by histopathological analyses. Histocompatibility antigen typing of 2 lesions was identical to a sample from peripheral blood. Accelerated regression was observed in 2 lesions treated by intralesional injection of betamethasone, while spontaneous regression was observed within 9 months in the remaining lesions without any treatment. Rapid growth, spontaneous regression and histological analyses in this case support the diagnosis of ‘infantile hemangioma-like vascular lesion'.
DOI: 10.6084/m9.figshare.5126374
title: Supplementary Material for: Whole Exome Sequencing to Identify Genetic Causes of Short Stature

description: <b><i>Background/Aims:</i></b> Short stature is a common reason for presentation to pediatric endocrinology clinics. However, for most patients, no cause for the short stature can be identified. As genetics plays a strong role in height, we sought to identify known and novel genetic causes of short stature. <b><i>Methods:</i></b> We recruited 14 children with severe short stature of unknown etiology. We conducted whole exome sequencing of the patients and their family members. We used an analysis pipeline to identify rare non-synonymous genetic variants that cause the short stature. <b><i>Results:</i></b> We identified a genetic cause of short stature in 5 of the 14 patients. This included cases of floating-harbor syndrome, Kenny-Caffey syndrome, the progeroid form of Ehlers-Danlos syndrome, as well as 2 cases of the 3-M syndrome. For the remaining patients, we have generated lists of candidate variants. <b><i>Conclusions:</i></b> Whole exome sequencing can help identify genetic causes of short stature in the context of defined genetic syndromes, but may be less effective in identifying novel genetic causes of short stature in individual families. Utilized in the clinic, whole exome sequencing can provide clinically relevant diagnoses for these patients. Rare syndromic causes of short stature may be underrecognized and underdiagnosed in pediatric endocrinology clinics.
DOI: 10.6084/m9.figshare.5126371.v1
title: Supplementary Material for: Infantile Hemangioma-Like Vascular Lesion in a 26-Year-Old Woman after Abortion

description: A 26-year-old woman (G2P1A1) presented with a 5-week history of multiple red marks on her body after a therapeutic abortion. A physical examination found 15 palpable red marks on her head, neck, chest, arms and legs. Proliferating endothelial cells, which expressed CD31, CD34, von Willebrand factor, but not Glut-1 and merosin, were observed in the lesional area by histopathological analyses. Histocompatibility antigen typing of 2 lesions was identical to a sample from peripheral blood. Accelerated regression was observed in 2 lesions treated by intralesional injection of betamethasone, while spontaneous regression was observed within 9 months in the remaining lesions without any treatment. Rapid growth, spontaneous regression and histological analyses in this case support the diagnosis of ‘infantile hemangioma-like vascular lesion'.
DOI: 10.6084/m9.figshare.5126377.v1
title: Supplementary Material for: Calcitonin Gene-Related Peptide Modulates the Production of Pro-Inflammatory Cytokines Associated with Periprosthetic Osteolysis by THP-1 Macrophage-Like Cells

description: <b><i>Objective:</i></b> An anti-resorptive impact of the neuropeptide calcitonin gene-related peptide (CGRP) on periprosthetic osteolysis, the leading cause of early prosthesis loosening, has been shown previously. In this study, the impact of CGRP on pro-inflammatory cytokine production associated with periprosthetic osteolysis was analysed using THP-1 macrophage-like cells. <b><i>Methods:</i></b> Cells were stimulated with ultra-high-molecular-weight polyethylene (UHMWPE) particles (cell-to-particle ratios of 1:100 and 1:500) and lipopolysaccharides (LPS; 1 µg/ml) to establish osteolytic conditions, and simultaneously treated with CGRP (10<sup>-8</sup>M). Receptor activator of nuclear factor-κB <i>(RANK)</i>, RANK ligand <i>(RANKL)</i> and tumour necrosis factor <i>(TNF)</i>-<i>a</i> mRNA expression were measured by quantitative RT-PCR. RANK protein was detected by Western blot. Secreted protein levels of TNF-a as well as interleukin (IL)-1ß and IL-6 were quantified in cell culture supernatants by ELISA and Bio-Plex cytokine assay, respectively. <b><i>Results:</i></b> Activation of macrophage-like cells failed to enhance the production of RANK but led to a dose- and time-dependent increase of <i>TNF</i>-<i>a</i> mRNA and secreted protein levels of TNF-a, IL-1ß and IL-6. Application of CGRP time-dependently suppressed <i>TNF-a</i> mRNA expression induced by low-particle concentrations and LPS, while both particle- and LPS-induced secretion of TNF-a was inhibited. A pronounced inhibitory effect of CGRP on LPS-induced cytokine production at 24 h of incubation was also observed with IL-1ß and IL-6. <b><i>Conclusions:</i></b> CGRP shows a time-dependent inhibitory effect on the secretion of osteolysis-associated pro-inflammatory cytokines, indicating an indirect anti-resorptive influence of the neuropeptide on both aseptic prosthesis loosening and bacterially induced bone resorption which might enhance the life time of total joint replacements.
DOI: 10.6084/m9.figshare.5126380.v1
title: Supplementary Material for: Polyploidy and Hybridization as Main Factors of Speciation: Complex Reticulate Evolution within the Grass Genus <b><i>Helictochloa</i></b>

description: To study the origin and evolution of naturally occurring polyploids, we performed phylogenetic analyses of nuclear ribosomal DNA spacers combined with molecular cytogenetics in 55 accessions of 27 taxa of the oat genus <i>Helictochloa</i>. A complex pattern of reticulate evolution was revealed with many diploid species and extensive polyploidy up to 20x. Altogether 11 groups of internal transcribed spacer (ITS) sequences can be distinguished. Sequences from 1-3 different ITS lineages were detected in polyploids. Cytogenetic data allow reconstruction of 8 basic monoploid chromosome sets. Six of these genomes occur in different combinations in the polyploid species. Two genomes are only found in diploids. Our sequence and karyological data highlight the occurrence of autopolyploidy and allopolyploidy, provide new information about the evolutionary history of taxa, and allow a more accurate systematic treatment of the concerned species. The geographical distribution of the 11 ITS lineages distinguished is highly structured and points to an origin of the genus in western Asia, presumably in grasslands like steppes or mountain steppes and meadows. The evolutionary basal lineages are of Asian, Minor Asian and east Mediterranean distribution and are present also in North America. The western and central parts of the Mediterranean and northern Europe harbor the modern lineages.