cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4704550.v3
title: Sinusoidal voltage protocols for rapid characterization of ion channel kinetics: supplementary code

description: Supplementary code for <strong>Sinusoidal voltage protocols for rapid characterization of ion channel kinetics</strong> by Kylie A. Beattie, Adam P. Hill, Rémi Bardenet, Yi Cui, Jamie I. Vandenberg, David J. Gavaghan, Teun P. de Boer and Gary R. Mirams.
DOI: 10.6084/m9.figshare.4704550.v4
title: Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics: supplementary code

description: Supplementary code for <strong>Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics</strong> by Kylie A. Beattie, Adam P. Hill, Rémi Bardenet, Yi Cui, Jamie I. Vandenberg, David J. Gavaghan, Teun P. de Boer and Gary R. Mirams.
DOI: 10.6084/m9.figshare.4702765
title: The Plasticity of Germ Cell Cancers and its Dependence on the Cellular Microenvironment

description: So far, the understanding of germ cell cancer (GCC) pathogenesis is based on a model, where seminomas and non-seminomas represent distinct entities although originating from a common precursor termed germ cell neoplasia <em>in situ</em> (GCNIS). Embryonal carcinomas (ECs), the stem cell population of the non-seminomas, is pluri- to totipotent and able to differentiate into cells of all three germ layers, giving rise to teratomas or tumours mimicking extraembryonic tissues (yolk sac tumours, choriocarcinomas). With regard to gene expression, (epi)genetics and histology, seminomas are highly similar to GCNIS and primordial germ cells, but limited in development. It remains elusive, whether this block in differentiation is controlled by cell intrinsic mechanisms or by signals from the surrounding microenvironment. Here, we reviewed the recent literature emphasizing the plasticity of GCCs, especially of seminomas. We propose that this plasticity is controlled by the microenvironment, allowing seminomas to transit into an EC or mixed non-seminoma and vice versa. We discuss several mechanisms and routes of reprogramming that might be responsible for this change in the cell fate. We finally integrate this plasticity into a new model of GCC pathogenesis, allowing for an alternative view on the dynamics of GCC development and progression.<br>
DOI: 10.6084/m9.figshare.4702711
title: Cross-CZO 16S rRNA 515f/806r reads

description: These are the mapping file, raw forward and reverse reads generated from 16S sequencing (515f/806r) of ~180 soils collected across the US within different critical zone observatories (CZOs). This study was designed to investigate changes in bacterial communities with soil depth across a wide range of geographic zones.
DOI: 10.6084/m9.figshare.4702765.v2
title: The Plasticity of Germ Cell Cancers and its Dependence on the Cellular Microenvironment

description: So far, the understanding of germ cell cancer (GCC) pathogenesis is based on a model, where seminomas and non-seminomas represent distinct entities although originating from a common precursor termed germ cell neoplasia <em>in situ</em> (GCNIS). Embryonal carcinomas (ECs), the stem cell population of the non-seminomas, is pluri- to totipotent and able to differentiate into cells of all three germ layers, giving rise to teratomas or tumours mimicking extraembryonic tissues (yolk sac tumours, choriocarcinomas). With regard to gene expression, (epi)genetics and histology, seminomas are highly similar to GCNIS and primordial germ cells, but limited in development. It remains elusive, whether this block in differentiation is controlled by cell intrinsic mechanisms or by signals from the surrounding microenvironment. Here, we reviewed the recent literature emphasizing the plasticity of GCCs, especially of seminomas. We propose that this plasticity is controlled by the microenvironment, allowing seminomas to transit into an EC or mixed non-seminoma and vice versa. We discuss several mechanisms and routes of reprogramming that might be responsible for this change in the cell fate. We finally integrate this plasticity into a new model of GCC pathogenesis, allowing for an alternative view on the dynamics of GCC development and progression.<br>
DOI: 10.6084/m9.figshare.4702708
title: Supplementary Material for: Benefits of an Oxygen Reservoir Cannula versus a Conventional Nasal Cannula during Exercise in Hypoxemic COPD Patients: A Crossover Trial

description: <b><i>Background:</i></b> The Oxymizer® is a special nasal cannula that provides a higher luminal diameter in combination with an incorporated oxygen (O<sub>2</sub>) reservoir. It is assumed that a higher O<sub>2</sub> concentration can be delivered breath by breath in order to increase oxygenation. <b><i>Objective:</i></b> We aimed to investigate the effects of the Oxymizer on endurance time in comparison to a conventional nasal cannula (CNC). <b><i>Methods:</i></b> Forty-three patients with severe chronic obstructive pulmonary disease (COPD, age 60 ± 9 years, FEV<sub>1</sub> 37 ± 16% pred.) and indications for LTOT were recruited during pulmonary rehabilitation for this cross-over study. After an initial maximal incremental cycle test, all patients performed 4 cycling endurance time tests at 70% of their peak work rate (twice with the Oxymizer and twice with a CNC, in reverse order). <b><i>Results:</i></b> The endurance time was significantly higher when patients cycled while using the Oxymizer in comparison to while using the CNC [858 ± 754 vs. 766 ± 652 s; between-group difference 92 s (95% confidence interval 32-152), p &lt; 0.001]. In addition to a longer cycling duration, O<sub>2</sub> saturation at isotime was significantly higher with the Oxymizer (93.5 ± 5.4 vs. 90.4 ± 5.3%; p = 0.027). Furthermore, there was a positive correlation (r = 0.427, p = 0.002) between the O<sub>2</sub> flow rate and improvements in the constant work rate test, showing greater improvements in favor of the Oxymizer in patients with a higher demand for O<sub>2</sub> (≥4 liters/min). <b><i>Conclusion:</i></b> We show that O<sub>2</sub> delivery via the Oxymizer is superior to a CNC with regard to endurance capacity and oxygenation during exercise in patients with severe COPD. It seems that patients with a higher demand for O<sub>2</sub> (≥4 liters/min), in particular, may benefit more from the use of the Oxymizer.
DOI: 10.6084/m9.figshare.4702687
title: Supplementary Material for: Methodology and Design of a National Epidemiological Study on Adult Neuromuscular Disease

description: <b><i>Background:</i></b> There have been no previous population-based studies of adult neuromuscular disease (NMD) in the Republic of Ireland (RoI). This article describes methods and case-ascertainment strategies used to identify patients with inherited and acquired NMD for the purpose of obtaining the prevalence of these disorders in the RoI. <b><i>Methods:</i></b> This epidemiological study was conducted between January 2012 and January 2014. Prospective and retrospective (until 1990) case identification of adults with inherited and acquired NMD have been carried out. Multiple countrywide patient identification sources including neuromuscular clinics, hospital neurology databases, the hospital in-patient enquiry (HIPE) system of each hospital and the records of Muscular Dystrophy Ireland, a nonprofit organisation, were used. <b><i>Results:</i></b> In total, 3,724 potential cases were identified. Of these, 1,083 were excluded because 869 cases represented duplicates or triplicates, 133 were coded incorrectly in HIPE, 74 patients were deceased and 7 patients had moved out of the country. The highest number of cases was identified in neurology databases and HIPE (1,724 and 884, respectively). A total of 2,641 individuals fulfilled the inclusion criteria and were included in the study. <b><i>Conclusion:</i></b> Detailed epidemiological data of this nature is difficult to acquire in the current structure of the Irish health service, requiring multiple sources including input from voluntary patient organisations. The development of a national patient registry for some or all of these conditions would greatly facilitate standardised data recording, giving a true picture of the burden of neuromuscular diseases in a population.
DOI: 10.6084/m9.figshare.4702681
title: Supplementary Material for: Current Practice of Cord Clamping in The Netherlands: A Questionnaire Study

description: <b><i>Background:</i></b> Recent meta-analyses recommend delayed cord clamping (DCC) after uncomplicated births as well as preterm births, but there is no clear definition of timing and uniform national guidelines are lacking. <b><i>Objective:</i></b> We aimed to investigate if guidelines for the timing of cord clamping (CC) are followed and what the national practice entails. <b><i>Methods:</i></b> A postal questionnaire concerning CC after uncomplicated vaginal, Caesarean term and preterm deliveries was sent to all midwifery practices (n = 526) and obstetrical departments (n = 94) in the Netherlands. <b><i>Results:</i></b> The response rate was 81% (500/620). CC protocols were present in 16 and 38% of midwifery and obstetric practices, respectively. Early cord clamping (ECC) was recommended in 54%, DCC in 33%, 6% indicated a specific time point and 7% did not specify. In current practice, DCC was applied after uncomplicated vaginal term deliveries in 90% and ECC in 6%, and no timing was specified in 4%. Midwives used DCC more often than obstetricians (97 vs. 75%). Cessation of cord pulsations was often (54%) used as a time point, 40% used a fixed time point, 2% waited for placental expulsion and 4% did not specify. ECC was preferred in obstetric practices after Caesarean deliveries (in 81%). In preterm births, ECC was practised by 36%, DCC by 54 and 10% did not specify. <b><i>Conclusion:</i></b> In the Netherlands, although often not protocolized, DCC is widely used after uncomplicated vaginal term and preterm deliveries, but not after Caesareans. Cessation of cord pulsation is often used as the time point for CC.
DOI: 10.6084/m9.figshare.4702687.v1
title: Supplementary Material for: Methodology and Design of a National Epidemiological Study on Adult Neuromuscular Disease

description: <b><i>Background:</i></b> There have been no previous population-based studies of adult neuromuscular disease (NMD) in the Republic of Ireland (RoI). This article describes methods and case-ascertainment strategies used to identify patients with inherited and acquired NMD for the purpose of obtaining the prevalence of these disorders in the RoI. <b><i>Methods:</i></b> This epidemiological study was conducted between January 2012 and January 2014. Prospective and retrospective (until 1990) case identification of adults with inherited and acquired NMD have been carried out. Multiple countrywide patient identification sources including neuromuscular clinics, hospital neurology databases, the hospital in-patient enquiry (HIPE) system of each hospital and the records of Muscular Dystrophy Ireland, a nonprofit organisation, were used. <b><i>Results:</i></b> In total, 3,724 potential cases were identified. Of these, 1,083 were excluded because 869 cases represented duplicates or triplicates, 133 were coded incorrectly in HIPE, 74 patients were deceased and 7 patients had moved out of the country. The highest number of cases was identified in neurology databases and HIPE (1,724 and 884, respectively). A total of 2,641 individuals fulfilled the inclusion criteria and were included in the study. <b><i>Conclusion:</i></b> Detailed epidemiological data of this nature is difficult to acquire in the current structure of the Irish health service, requiring multiple sources including input from voluntary patient organisations. The development of a national patient registry for some or all of these conditions would greatly facilitate standardised data recording, giving a true picture of the burden of neuromuscular diseases in a population.
DOI: 10.6084/m9.figshare.4702666
title: Supplementary Material for: Clinical Evaluation of an Image-Guided Cochlear Implant Programming Strategy

description: The cochlear implant (CI) has been labeled the most successful neural prosthesis. Despite this success, a significant number of CI recipients experience poor speech understanding, and, even among the best performers, restoration to normal auditory fidelity is rare. While significant research efforts have been devoted to improving stimulation strategies, few developments have led to significant hearing improvement over the past two decades. We have recently introduced image processing techniques that open a new direction for advancement in this field by making it possible, for the first time, to determine the position of implanted CI electrodes relative to the nerves they stimulate using computed tomography images. In this article, we present results of an image-guided, patient-customized approach to stimulation that utilizes the electrode position information our image processing techniques provide. This approach allows us to identify electrodes that cause overlapping stimulation patterns and to deactivate them from a patient's map. This individualized mapping strategy yields significant improvement in speech understanding in both quiet and noise as well as improved spectral resolution in the 68 adult CI recipients studied to date. Our results indicate that image guidance can improve hearing outcomes for many existing CI recipients without requiring additional surgery or the use of ‘experimental' stimulation strategies, hardware or software.
DOI: 10.6084/m9.figshare.4702672
title: Supplementary Material for: Influence of Gestational Age on Dead Space and Alveolar Ventilation in Preterm Infants Ventilated with Volume Guarantee

description: <b><i>Background:</i></b> Ventilated preterm infant lungs are vulnerable to overdistension and underinflation. The optimal ventilator-delivered tidal volume (<i>V</i><sub>T</sub>) in these infants is unknown and may depend on the extent of alveolarisation at birth. <b><i>Objectives:</i></b> We aimed to calculate respiratory dead space (<i>V</i><sub>D</sub>) from the molar mass (MM) signal of an ultrasonic flowmeter (<i>V</i><sub>D,MM</sub>) in very preterm infants on volume-targeted ventilation (<i>V</i><sub>T</sub> target, 4-5 ml/kg) and to study the association between gestational age (GA) and <i>V</i><sub>D,MM</sub>-to-<i>V</i><sub>T</sub> ratio (<i>V</i><sub>D,MM</sub>/<i>V</i><sub>T</sub>), alveolar tidal volume (<i>V</i><sub>A</sub>) and alveolar minute volume (AMV). <b><i>Methods:</i></b> This was a single-centre, prospective, observational, cohort study in a neonatal intensive care unit. Tidal breathing analysis was performed in ventilated very preterm infants (GA range 23-32 weeks) on day 1 of life. <b><i>Results:</i></b> Valid measurements were obtained in 43/51 (87%) infants. Tidal breathing variables were analysed using multivariable linear regression. <i>V</i><sub>D,MM</sub>/<i>V</i><sub>T</sub> was negatively associated with GA after adjusting for birth weight Z score (p<i> &lt;</i> 0.001, R<sup>2</sup> = 0.26). This association was primarily influenced by the appliance dead space. Despite similar <i>V</i><sub>T</sub>/kg and <i>V</i><sub>A</sub>/kg across all studied infants, respiratory rate and AMV/kg increased with GA. <b><i>Conclusions:</i></b><i>V</i><sub>D,app</sub> rather than anatomical <i>V</i><sub>D</sub> is the major factor influencing increased <i>V</i><sub>D,MM</sub>/<i>V</i><sub>T</sub> at a younger GA. A volume guarantee setting of 4-5 ml/kg in the Dräger Babylog® 8000 plus ventilator may be inappropriate as a universal target across the GA range of 23-32 weeks. Differences between measured and set <i>V</i><sub>T</sub> and the dependence of this difference on GA require further investigation.
DOI: 10.6084/m9.figshare.4702645
title: PowerPoint Slides for: Targeting Immunity in End-Stage Renal Disease

description: <b><i>Background:</i></b> Despite the stable incidence of end-stage renal disease (ESRD), it continues to be associated with an unacceptably high cardiovascular risk. <b><i>Summary:</i></b> ESRD is characterized by enhanced oxidative stress and severe inflammation, which boost cardiovascular risk, thus increasing cardiovascular-associated mortality rate. While substantial effort has been made in the technological innovation of dialytic techniques, few significant advances have been made to reduce inflammation in patients with ESRD. Indeed, this contrasts with the extensive scientific breakthroughs made in the basic field of science in targeting inflammation. There is thus a pressing need for clinical trials to test the effect of reducing inflammation in patients with ESRD. Here, we will revisit the negative effect of ESRD on inflammation and explore the impact of enhanced inflammation on cardiovascular outcomes and survival in patients with ESRD. Finally, we will discuss the need for clinical trials that target inflammation in ESRD, as well as weigh potential disadvantages and offer novel innovative approaches. <b><i>Key Message:</i></b> We will try to understand why the issue of inflammation has not been successfully addressed thus far in patients with ESRD, while at the same time weighing the potential disadvantages and offering novel innovative approaches for targeting inflammation in patients with ESRD.
DOI: 10.6084/m9.figshare.4702645.v1
title: PowerPoint Slides for: Targeting Immunity in End-Stage Renal Disease

description: <b><i>Background:</i></b> Despite the stable incidence of end-stage renal disease (ESRD), it continues to be associated with an unacceptably high cardiovascular risk. <b><i>Summary:</i></b> ESRD is characterized by enhanced oxidative stress and severe inflammation, which boost cardiovascular risk, thus increasing cardiovascular-associated mortality rate. While substantial effort has been made in the technological innovation of dialytic techniques, few significant advances have been made to reduce inflammation in patients with ESRD. Indeed, this contrasts with the extensive scientific breakthroughs made in the basic field of science in targeting inflammation. There is thus a pressing need for clinical trials to test the effect of reducing inflammation in patients with ESRD. Here, we will revisit the negative effect of ESRD on inflammation and explore the impact of enhanced inflammation on cardiovascular outcomes and survival in patients with ESRD. Finally, we will discuss the need for clinical trials that target inflammation in ESRD, as well as weigh potential disadvantages and offer novel innovative approaches. <b><i>Key Message:</i></b> We will try to understand why the issue of inflammation has not been successfully addressed thus far in patients with ESRD, while at the same time weighing the potential disadvantages and offering novel innovative approaches for targeting inflammation in patients with ESRD.
DOI: 10.6084/m9.figshare.4702597
title: Supplementary Material for: Bilberry-Derived Anthocyanins Prevent IFN-γ-Induced Pro-Inflammatory Signalling and Cytokine Secretion in Human THP-1 Monocytic Cells

description: <b><i>Background/Aims:</i></b> Anthocyanins are plant-derived dietary components that are highly abundant, for example, in bilberries. We have previously demonstrated that anthocyanins exert anti-inflammatory properties in mouse colitis models and ameliorate disease activity in ulcerative colitis patients. Here, we studied the molecular mechanisms through which anthocyanin-containing bilberry extract (BE) exerts anti-inflammatory effects in human monocytic THP-1 cells. <b><i>Methods:</i></b> THP-1 cells were pre-incubated with BE 20 min prior to TNF-a or IFN-γ (100 ng/ml each) stimulation. Signalling protein activation was studied by Western blotting, mRNA expression by quantitative PCR and cytokine secretion by ELISA. <b><i>Results:</i></b> IFN-γ-induced phosphorylation of STAT1 and STAT3 was significantly reduced by BE co-treatment. Consequently, levels of mRNA expression and/or cytokine secretion of MCP-1, IL-6, TNF-a, ICAM-1, and T-bet were lower with BE co-treatment. In contrast, BE enhanced TNF-a-mediated p65-NF-γB phosphorylation but reduced ERK1/2 phosphorylation. BE co-treatment further increased TNF-a-induced mRNA expression and secretion of NF-γB target genes, such as IL-6, IL-8, and MCP-1, while mRNA levels of ICAM-1 were reduced. <b><i>Conclusions:</i></b> BE co-treatment reduced IFN-γ-induced signal protein activation, pro-inflammatory gene expression, and cytokine secretion, whereas it enhanced TNF-a-induced responses. These findings suggest a distinct role for anthocyanins in modulating inflammatory responses that need to be further studied to fully understand anthocyanin-mediated effects.
DOI: 10.6084/m9.figshare.4702615
title: Supplementary Material for: Acute Severe Methotrexate Toxicity in Patients with Psoriasis: A Case Series and Discussion

description: <b><i>Background:</i></b> Methotrexate (MTX) is considered a relatively safe drug when prescribed at low-dose regimens not exceeding 25 mg/week. Severe acute toxicity is rare and presents with mucositis, cutaneous ulceration and pancytopenia. Most cases occur as the result of inadvertent overdosing due to erroneously taking the drug daily. However, concomitant factors such as older age, co-medication and renal failure may increase the drug's toxicity. <b><i>Case Reports:</i></b> We report four consecutive cases of acute MTX toxicity in patients with psoriasis vulgaris. In three patients, MTX was erroneously taken daily for 2-4 weeks. All three patients recovered following MTX withdrawal and intensive treatment. The fourth patient was taking 7.5 mg weekly MTX as prescribed, but had concomitant factors and died. <b><i>Conclusion:</i></b> Although low-dose MTX appears to be a safe medication, acute MTX toxicity can be a life-threatening emergency. Greater awareness of possible MTX toxicity is still needed for its prevention, early diagnosis and management.
DOI: 10.6084/m9.figshare.4702615.v1
title: Supplementary Material for: Acute Severe Methotrexate Toxicity in Patients with Psoriasis: A Case Series and Discussion

description: <b><i>Background:</i></b> Methotrexate (MTX) is considered a relatively safe drug when prescribed at low-dose regimens not exceeding 25 mg/week. Severe acute toxicity is rare and presents with mucositis, cutaneous ulceration and pancytopenia. Most cases occur as the result of inadvertent overdosing due to erroneously taking the drug daily. However, concomitant factors such as older age, co-medication and renal failure may increase the drug's toxicity. <b><i>Case Reports:</i></b> We report four consecutive cases of acute MTX toxicity in patients with psoriasis vulgaris. In three patients, MTX was erroneously taken daily for 2-4 weeks. All three patients recovered following MTX withdrawal and intensive treatment. The fourth patient was taking 7.5 mg weekly MTX as prescribed, but had concomitant factors and died. <b><i>Conclusion:</i></b> Although low-dose MTX appears to be a safe medication, acute MTX toxicity can be a life-threatening emergency. Greater awareness of possible MTX toxicity is still needed for its prevention, early diagnosis and management.
DOI: 10.6084/m9.figshare.4702555
title: Haggis data: individual plasticity

description: Simulated data sets for use with Tutorial II, 'Multivariate modelling for individual plasticity variation', associated with 'Avoiding the misuse of BLUP in behavioural ecology'.<br>The file 'aggression.csv' provides the data for the first part of the tutorial, using random regression to model individual variation in how aggressive behaviour changes in response to the size of opponent. This data includes repeated measures of aggression at each opponent size for every individual, along with body size and fitness measurements.<br>File 'aggression_CS.csv' presents the same data having been reformatted to suit the 'character state' approach used in the second part of the tutorial. Note that 'fitness' has already been standardised to relative fitness in this set.