cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5097316
title: Supplementary Material for: Pulmonary Rehabilitation Outcomes after Single or Double Lung Transplantation in Patients with Chronic Obstructive Pulmonary Disease or Interstitial Lung Disease

description: <b><i>Background:</i></b> Pulmonary rehabilitation (PR) following lung transplantation (LTx) has been shown to be effective with regard to exercise capacity and health-related quality of life (HRQL). However, outcome data is limited with respect to LTx as a population. Differences concerning the effects of PR in patients with single LTx (SLTx) or double LTx (DLTx) have not been studied yet. <b><i>Objectives:</i></b> The aim was to compare possible differences concerning PR outcomes between SLTx and DLTx. <b><i>Methods:</i></b> In a retrospective analysis (period: 1997-2016), data from 722 patients with either chronic obstructive pulmonary disease (COPD; SLTx: <i>n</i> = 129, FEV<sub>1</sub> 51 ± 17% pred.; DLTx: <i>n</i> = 204, FEV<sub>1</sub> 74 ± 20% pred.) or interstitial lung disease (ILD; SLTx: <i>n</i> = 135, FVC 58 ± 18% pred.; DLTx: <i>n</i> = 254, FVC 63 ± 18% pred.) after LTx were included. All patients underwent a specialized inpatient PR program. The data of the 6-minute walk distance (6MWD) and HRQL (physical [PCS] and mental [MCS] component summary of the SF- 36 questionnaire) were analyzed. <b><i>Results:</i></b> Independently from the procedure and pretransplant diagnosis, patients significantly (<i>p</i> &lt; 0.05) improved the 6MWD without any differences between SLTx and DLTx (COPD: SLTx: +109 ± 68 m, DLTx: +117 ± 82 m; ILD: SLTx: +115 ± 80 m, DLTx: +132 ± 77 m). The PCS (COPD: SLTx: +9 ± 9 points, DLTx: +7 ± 9 points; ILD: SLTx: +6 ± 9 points, DLTx: +9 ± 9 points) and MCS (COPD: SLTx: +8 ± 15 points, DLTx: +7 ± 15 points; ILD: SLTx: +10 ± 13 points, DLTx: +8 ± 12 points) also improved significantly without any group differences. <b><i>Conclusions:</i></b> LTx patients with a pretransplant diagnosis of COPD or ILD all benefitted significantly and with clinical relevance with regard to exercise capacity and HRQL from an inpatient PR performed within 1 year postoperatively. PR outcomes were similar regardless of SLTx or DLTx.
DOI: 10.6084/m9.figshare.5097322.v1
title: Supplementary Material for: Outcomes in Melanoma Patients Treated with BRAF/MEK-Directed Therapy or Immune Checkpoint Inhibition Stratified by Clinical Trial versus Standard of Care

description: <b><i>Objectives:</i></b> Since 2011, metastatic melanoma treatment has evolved with commercial approval of BRAF- and MEK-targeted therapy and CTLA-4- and PD-1-blocking antibodies (immune checkpoint inhibitors, ICI). While novel therapies have demonstrated improved prognosis in clinical trials, few studies have examined the evolution of prognosis and toxicity of these drugs among an unselected population. We assess whether survival and toxicity reported in trials, which typically exclude most patients with brain metastases and poor performance status, are recapitulated within a commercial access population. <b><i>Methods:</i></b> 182 patients diagnosed with stage IV melanoma from July 2006 to December 2013 and treated with BRAF- and/or MEK-targeted therapy or ICI were prospectively studied. Outcomes and clinicopathologic differences between trial and commercial cohorts were assessed. <b><i>Results:</i></b> Patients receiving commercial therapy (vs. on trial) had poorer prognostic features (i.e., brain metastases) and lower median overall survival (mOS) when assessed across all treatments (9.2 vs. 17.5 months, <i>p</i> = 0.0027). While toxicity within trial and commercial cohorts did not differ, patients who experienced toxicity had increased mOS (<i>p</i> &lt; 0.001), irrespective of stratification by trial status or therapy. <b><i>Conclusion</i></b>: Metastatic melanoma patients receiving commercial treatment may represent a different clinical population with poor prognostic features compared to trial patients. Toxicity may prognosticate treatment benefit.
DOI: 10.6084/m9.figshare.5097286
title: Data References from Hierarchical complexity and the size limits of life

description: References for sizes in Data File
DOI: 10.6084/m9.figshare.5097274
title: Data File from Hierarchical complexity and the size limits of life

description: Size (cubic mm) and complexity level for all taxa used in this study
DOI: 10.6084/m9.figshare.5097142
title: Supplementary Material for: Weight Bias: A Systematic Review of Characteristics and Psychometric Properties of Self-Report Questionnaires

description: <b><i>Background:</i></b> People living with overweight and obesity often experience weight-based stigmatization. Investigations of the prevalence and correlates of weight bias and evaluation of weight bias reduction interventions depend upon psychometrically-sound measurement. Our paper is the first to comprehensively evaluate the psychometric properties, use of people-first language within items, and suitability for use with various populations of available self-report measures of weight bias. <b><i>Methods:</i></b> We searched five electronic databases to identify English-language self-report questionnaires of weight bias. We rated each questionnaire's psychometric properties based on initial validation reports and subsequent use, and examined item language. <b><i>Results:</i></b> Our systematic review identified 40 original self-report questionnaires. Most questionnaires were brief, demonstrated adequate internal consistency, and tapped key cognitive and affective dimensions of weight bias such as stereotypes and blaming. Current psychometric evidence is incomplete for many questionnaires, particularly with regard to the properties of test-retest reliability, sensitivity to change as well as discriminant and structural validity. Most questionnaires were developed prior to debate surrounding terminology preferences, and do not employ people-first language in the items administered to participants. <b><i>Conclusions:</i></b> We provide information and recommendations for clinicians and researchers in selecting psychometrically sound measures of weight bias for various purposes and populations, and discuss future directions to improve measurement of this construct.
DOI: 10.6084/m9.figshare.5097121
title: Supplementary Material for: IL-37 Causes Excessive Inflammation and Tissue Damage in Murine Pneumococcal Pneumonia

description: <i>Streptococcus pneumoniae </i>infections can lead to severe complications with excessive immune activation and tissue damage. Interleukin-37 (IL-37) has gained importance as a suppressor of innate and acquired immunity, and its effects have been therapeutic as they prevent tissue damage in autoimmune and inflammatory diseases. By using RAW macrophages, stably transfected with human IL-37, we showed a 70% decrease in the cytokine levels of IL-6, TNF-α, and IL-1β, and a 2.2-fold reduction of the intracellular killing capacity of internalized pneumococci in response to pneumococcal infection. In a murine model of infection with <i>S. pneumoniae</i>, using mice transgenic for human IL-37b (IL-37tg), we observed an initial decrease in cytokine expression of IL-6, TNF-α, and IL-1β in the lungs, followed by a late-phase enhancement of pneumococcal burden and subsequent increase of proinflammatory cytokine levels. Additionally, a marked increase in recruitment of alveolar macrophages and neutrophils was noted, while TRAIL mRNA was reduced 3-fold in lungs of IL-37tg mice, resulting in necrotizing pneumonia with augmented death of infiltrating neutrophils, enhanced bacteremic spread, and increased mortality. In conclusion, we have identified that IL-37 modulates several core components of a successful inflammatory response to pneumococcal pneumonia, which lead to increased inflammation, tissue damage, and mortality.
DOI: 10.6084/m9.figshare.5097121.v1
title: Supplementary Material for: IL-37 Causes Excessive Inflammation and Tissue Damage in Murine Pneumococcal Pneumonia

description: <i>Streptococcus pneumoniae </i>infections can lead to severe complications with excessive immune activation and tissue damage. Interleukin-37 (IL-37) has gained importance as a suppressor of innate and acquired immunity, and its effects have been therapeutic as they prevent tissue damage in autoimmune and inflammatory diseases. By using RAW macrophages, stably transfected with human IL-37, we showed a 70% decrease in the cytokine levels of IL-6, TNF-α, and IL-1β, and a 2.2-fold reduction of the intracellular killing capacity of internalized pneumococci in response to pneumococcal infection. In a murine model of infection with <i>S. pneumoniae</i>, using mice transgenic for human IL-37b (IL-37tg), we observed an initial decrease in cytokine expression of IL-6, TNF-α, and IL-1β in the lungs, followed by a late-phase enhancement of pneumococcal burden and subsequent increase of proinflammatory cytokine levels. Additionally, a marked increase in recruitment of alveolar macrophages and neutrophils was noted, while TRAIL mRNA was reduced 3-fold in lungs of IL-37tg mice, resulting in necrotizing pneumonia with augmented death of infiltrating neutrophils, enhanced bacteremic spread, and increased mortality. In conclusion, we have identified that IL-37 modulates several core components of a successful inflammatory response to pneumococcal pneumonia, which lead to increased inflammation, tissue damage, and mortality.
DOI: 10.6084/m9.figshare.5096608
title: Supplementary Information.docx

description: Contain supplementary information linked to main manuscript.<br>
DOI: 10.6084/m9.figshare.5096599
title: Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles

description: In our previous study, we have observed that the isolated coat proteins (CP) of the Potyvirus Potato Virus A (PVA) virions exhibit an intrinsic tendency to self-associate into various multimeric forms containing some fractions of cross-β-structure. In this report, we studied the effect of solution conditions on the structure and dissociation of isolated PVA CP using a number of complementary physicochemical methods. Analysis of the structure of PVA CP in solution was performed by limited proteolysis with MALDI-TOF mass spectrometry analysis, transmission electron microscopy, intrinsic fluorescence spectroscopy, and synchrotron small angle X-ray scattering (SAXS). Overall structural characteristics of PVA CP obtained by combination of these methods and <i>ab initio</i> shape reconstruction by SAXS show that PVA CP forms large multi-subunit particles. We demonstrate that a mixture of compact virus-like particles (VLP) longer than 30 nm is assembled on dialysis of isolated CP into neutral pH buffer (at low ionic strength). Under conditions of high ionic strength (0.5 M NaCl) and high pH (pH 10.5), PVA dissociates into low compactness oval-shaped particles of approximately 30 subunits (20–30 nm). The results of limited trypsinolysis of these particles (enzyme/substrate ratio 1:100, 30 min) showed the existence of non-cleavable core-fragment, consisting of 137 amino acid residues. Trypsin treatment removed only a short N-terminal fragment in the intact virions. These particles are readily reassembled into regular VLPs by changing pH back to neutral. It is possible that these particles may represent some kind of intermediate in PVA assembly <i>in vitro</i> and <i>in vivo</i>.
DOI: 10.6084/m9.figshare.5096608.v1
title: Supplementary Information.docx

description: Contain supplementary information linked to main manuscript.<br>
DOI: 10.6084/m9.figshare.5096599.v2
title: Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles

description: In our previous study, we have observed that the isolated coat proteins (CP) of the Potyvirus Potato Virus A (PVA) virions exhibit an intrinsic tendency to self-associate into various multimeric forms containing some fractions of cross-β-structure. In this report, we studied the effect of solution conditions on the structure and dissociation of isolated PVA CP using a number of complementary physicochemical methods. Analysis of the structure of PVA CP in solution was performed by limited proteolysis with MALDI-TOF mass spectrometry analysis, transmission electron microscopy, intrinsic fluorescence spectroscopy, and synchrotron small angle X-ray scattering (SAXS). Overall structural characteristics of PVA CP obtained by combination of these methods and <i>ab initio</i> shape reconstruction by SAXS show that PVA CP forms large multi-subunit particles. We demonstrate that a mixture of compact virus-like particles (VLP) longer than 30 nm is assembled on dialysis of isolated CP into neutral pH buffer (at low ionic strength). Under conditions of high ionic strength (0.5 M NaCl) and high pH (pH 10.5), PVA dissociates into low compactness oval-shaped particles of approximately 30 subunits (20–30 nm). The results of limited trypsinolysis of these particles (enzyme/substrate ratio 1:100, 30 min) showed the existence of non-cleavable core-fragment, consisting of 137 amino acid residues. Trypsin treatment removed only a short N-terminal fragment in the intact virions. These particles are readily reassembled into regular VLPs by changing pH back to neutral. It is possible that these particles may represent some kind of intermediate in PVA assembly <i>in vitro</i> and <i>in vivo</i>.
DOI: 10.6084/m9.figshare.5096599.v1
title: Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles

description: In our previous study, we have observed that the isolated coat proteins (CP) of the Potyvirus Potato Virus A (PVA) virions exhibit an intrinsic tendency to self-associate into various multimeric forms containing some fractions of cross-β-structure. In this report, we studied the effect of solution conditions on the structure and dissociation of isolated PVA CP using a number of complementary physicochemical methods. Analysis of the structure of PVA CP in solution was performed by limited proteolysis with MALDI-TOF mass spectrometry analysis, transmission electron microscopy, intrinsic fluorescence spectroscopy, and synchrotron small angle X-ray scattering (SAXS). Overall structural characteristics of PVA CP obtained by combination of these methods and <i>ab initio</i> shape reconstruction by SAXS show that PVA CP forms large multi-subunit particles. We demonstrate that a mixture of compact virus-like particles (VLP) longer than 30 nm is assembled on dialysis of isolated CP into neutral pH buffer (at low ionic strength). Under conditions of high ionic strength (0.5 M NaCl) and high pH (pH 10.5), PVA dissociates into low compactness oval-shaped particles of approximately 30 subunits (20–30 nm). The results of limited trypsinolysis of these particles (enzyme/substrate ratio 1:100, 30 min) showed the existence of non-cleavable core-fragment, consisting of 137 amino acid residues. Trypsin treatment removed only a short N-terminal fragment in the intact virions. These particles are readily reassembled into regular VLPs by changing pH back to neutral. It is possible that these particles may represent some kind of intermediate in PVA assembly <i>in vitro</i> and <i>in vivo</i>.
DOI: 10.6084/m9.figshare.5096455
title: MUSEC_Briefings_Archive

description: Archive of the MUSEC Briefings on educational and clinical interventions for children with developmental disorders. Debunking pseudoscience, and pointing the way to evidence-based interventions.<br>
DOI: 10.6084/m9.figshare.5096440
title: Dataset for: Dynamic Nuclear Polarization Studies of Nitroxyl Spin Probes in Agarose gel Using Overhauser-enhanced Magnetic Resonance Imaging

description: Agarose is a tissue-equivalent material and its imaging characteristics similar to those of real tissues. Hence the dynamic nuclear polarization studies of carboxy-PROXYL in agarose gel were carried out. The DNP parameters such as spin lattice relaxation time, longitudinal relaxivity, leakage factor, saturation parameter and coupling parameter were estimated for 2 mM carboxy-PROXYL in PBS solution and water/agarose mixture (99:1). From these results, the spin probe concentration was optimized as 2 mM, and the reduction in enhancement was observed for carboxy-PROXYL in water/agarose mixture (99:1) compared with PBS solution. Phantom imaging was also performed with 2 mM concentration of carboxy-PROXYL in various concentrations of agarose gel at various radio frequency power levels. The results from the dynamic nuclear polarization measurements agree well with the phantom imaging results. These results pave the way for designing model system for human tissues suited to the biological applications of electron spin resonance/ Overhauser-enhanced magnetic resonance imaging.
DOI: 10.6084/m9.figshare.5096422
title: Dataset for: Measuring Mimicry: General Corticospinal Facilitation During Observation of Naturalistic Behaviour

description: Mimicry of others’ postures and behaviours forms an implicit yet indispensable component of social interactions. However, whereas numerous behavioural studies have investigated the occurrence of mimicry and its social sensitivity, the underlying neurocognitive mechanisms remain elusive. In this study, single pulse transcranial magnetic stimulation was used to measure corticospinal facilitation during a naturalistic behaviour observation task adapted from the behavioural mimicry literature. Motor evoked potentials (MEPs) in participants’ right hands were measured as they observed stimulus videos of a confederate describing photographs. MEPs were recorded while confederates were and were not carrying out hand and leg behaviours that also differed in spatial extent (i.e. large behaviours: face rubbing and leg crossing; small behaviours: finger tapping and foot bouncing). However, the cover task instructions did not refer to the confederate's behaviour but instead required participants to focus on the confederates’ photograph descriptions in order to later perform a recognition test. A general arousal effect was found, with higher MEPs during stimulus video observation than during a fixation-cross baseline, regardless of whether or not the confederate was carrying out a behaviour at the time of the pulse. When controlling for this general arousal effect, results showed that MEPs during observation of the larger two behaviours were significantly higher than the smaller two behaviours, irrespective of effector. Thus, by using a controlled yet naturalistic paradigm, this study suggests that general sensorimotor arousal during social interactions could play a role in implicit behavioural mimicry.
DOI: 10.6084/m9.figshare.5096428
title: Dataset for: Early life decline in neurogenesis markers and age-related changes of TrkB splice variant expression in the human subependymal zone

description: Neurogenesis in the subependymal zone (SEZ) declines across the human lifespan and reduced local neurotrophic support is speculated to be a contributing factor. While tyrosine receptor kinase B (TrkB) signalling is critical for neuronal differentiation, maturation and survival, little is known about subependymal TrkB expression changes during postnatal human life. In this study, we used quantitative PCR and in situ hybridisation to determine expression of the cell proliferation marker Ki67, the immature neuron marker doublecortin (DCX) and both full-length (TrkB-TK+) and truncated TrkB receptors (TrkB-TK-) in the human SEZ from infancy to middle age (n=26-35, 41 days–43 years). We further measured TrkB-TK+ and TrkB-TK- mRNAs in the SEZ from young adulthood into aging (n=50, 21-103 years), and related their transcript levels to neurogenic and glial cell markers. Ki67, DCX and both TrkB splice variant mRNAs significantly decreased in the SEZ from infancy to middle age. In contrast, TrkB-TK- mRNA increased in the SEZ from young adulthood into aging, whereas TrkB-TK+ mRNA remained stable. TrkB-TK- mRNA positively correlated with expression of neural precursor (glial fibrillary acidic protein delta and achaete-scute homolog 1) and glial cell markers (vimentin and pan glial fibrillary acidic protein). TrkB-TK+ mRNA positively correlated with expression of neuronal cell markers (DCX and tubulin beta 3 class III). Our results indicate that cells residing in the human SEZ maintain their responsiveness to neurotrophins; however, this capability may change across postnatal life. We suggest that TrkB splice variants may differentially influence neuronal and glial differentiation in the human SEZ.
DOI: 10.6084/m9.figshare.5096440.v1
title: Dataset for: Dynamic Nuclear Polarization Studies of Nitroxyl Spin Probes in Agarose gel Using Overhauser-enhanced Magnetic Resonance Imaging

description: Agarose is a tissue-equivalent material and its imaging characteristics similar to those of real tissues. Hence the dynamic nuclear polarization studies of carboxy-PROXYL in agarose gel were carried out. The DNP parameters such as spin lattice relaxation time, longitudinal relaxivity, leakage factor, saturation parameter and coupling parameter were estimated for 2 mM carboxy-PROXYL in PBS solution and water/agarose mixture (99:1). From these results, the spin probe concentration was optimized as 2 mM, and the reduction in enhancement was observed for carboxy-PROXYL in water/agarose mixture (99:1) compared with PBS solution. Phantom imaging was also performed with 2 mM concentration of carboxy-PROXYL in various concentrations of agarose gel at various radio frequency power levels. The results from the dynamic nuclear polarization measurements agree well with the phantom imaging results. These results pave the way for designing model system for human tissues suited to the biological applications of electron spin resonance/ Overhauser-enhanced magnetic resonance imaging.
DOI: 10.6084/m9.figshare.5096422.v1
title: Dataset for: Measuring Mimicry: General Corticospinal Facilitation During Observation of Naturalistic Behaviour

description: Mimicry of others’ postures and behaviours forms an implicit yet indispensable component of social interactions. However, whereas numerous behavioural studies have investigated the occurrence of mimicry and its social sensitivity, the underlying neurocognitive mechanisms remain elusive. In this study, single pulse transcranial magnetic stimulation was used to measure corticospinal facilitation during a naturalistic behaviour observation task adapted from the behavioural mimicry literature. Motor evoked potentials (MEPs) in participants’ right hands were measured as they observed stimulus videos of a confederate describing photographs. MEPs were recorded while confederates were and were not carrying out hand and leg behaviours that also differed in spatial extent (i.e. large behaviours: face rubbing and leg crossing; small behaviours: finger tapping and foot bouncing). However, the cover task instructions did not refer to the confederate's behaviour but instead required participants to focus on the confederates’ photograph descriptions in order to later perform a recognition test. A general arousal effect was found, with higher MEPs during stimulus video observation than during a fixation-cross baseline, regardless of whether or not the confederate was carrying out a behaviour at the time of the pulse. When controlling for this general arousal effect, results showed that MEPs during observation of the larger two behaviours were significantly higher than the smaller two behaviours, irrespective of effector. Thus, by using a controlled yet naturalistic paradigm, this study suggests that general sensorimotor arousal during social interactions could play a role in implicit behavioural mimicry.