cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4541371
title: Droplet-based microfluidics detector for bioaerosol detection

description: Detection of bioaerosols is important in fields ranging from environmental health monitoring to biosurveillance, and current detector weaknesses have motivated the development of new technologies. In this work, a detector was built, which applies the principles of droplet microfluidics to bioaerosol detection. Droplet microfluidics is a subfield of microfluidics based on the creation of monodisperse microdroplets with compartmentalized reagents and supports enhanced assays and fluidic manipulations. The bioaerosol detector operates by aerodynamically focusing aerosols directly into these droplets to harness the benefits of the microreactor environment. A breadboard detector system, which consisted of an aerodynamic focusing lens, aerosol-focusing capillary, microfluidic droplet chip, and optical microscope, was constructed. Computational fluid dynamic simulations and Lagrangian particle tracking modeling were conducted to identify the optimal conditions for focusing. Preliminary experiments, where aerosols were deposited onto a solid substrate, demonstrated sub 200-µm spot diameters for aerodynamic diameters of 2–5 µm. Test aerosols were then generated, and collected into the microfluidic liquid interface on the chip as verified by microscopy. Recovery efficiency of the aerosols was dependent on aerosol size and ranged from about 27% to nearly 100%. Finally, to prove bioaerosol collection and detection, a droplet propidium iodide (PI) assay was performed: the system distinguished between <i>E. coli</i> and non-biological aerosols within 20 s. Overall, this work established the technique of direct collection of bioaerosols into a convenient droplet microfluidic platform for detection. Copyright © 2017 The Johns Hopkins University Applied Physics Laboratory
DOI: 10.6084/m9.figshare.4541371.v1
title: Droplet-based microfluidics detector for bioaerosol detection

description: Detection of bioaerosols is important in fields ranging from environmental health monitoring to biosurveillance, and current detector weaknesses have motivated the development of new technologies. In this work, a detector was built, which applies the principles of droplet microfluidics to bioaerosol detection. Droplet microfluidics is a subfield of microfluidics based on the creation of monodisperse microdroplets with compartmentalized reagents and supports enhanced assays and fluidic manipulations. The bioaerosol detector operates by aerodynamically focusing aerosols directly into these droplets to harness the benefits of the microreactor environment. A breadboard detector system, which consisted of an aerodynamic focusing lens, aerosol-focusing capillary, microfluidic droplet chip, and optical microscope, was constructed. Computational fluid dynamic simulations and Lagrangian particle tracking modeling were conducted to identify the optimal conditions for focusing. Preliminary experiments, where aerosols were deposited onto a solid substrate, demonstrated sub 200-µm spot diameters for aerodynamic diameters of 2–5 µm. Test aerosols were then generated, and collected into the microfluidic liquid interface on the chip as verified by microscopy. Recovery efficiency of the aerosols was dependent on aerosol size and ranged from about 27% to nearly 100%. Finally, to prove bioaerosol collection and detection, a droplet propidium iodide (PI) assay was performed: the system distinguished between <i>E. coli</i> and non-biological aerosols within 20 s. Overall, this work established the technique of direct collection of bioaerosols into a convenient droplet microfluidic platform for detection. Copyright © 2017 The Johns Hopkins University Applied Physics Laboratory
DOI: 10.6084/m9.figshare.4541236
title: Is my research right? Surviving in a post-expert world

description: This is a talk motivating why all researchers should learn enough about research software to survive in a post-expert world, for the research software management, sharing and sustainability workshop series. #researchsoftware<br>This talk was given as a keynote at the workshops at the British Library (12th January 2017) and the University of Cambridge (16th January 2017).
DOI: 10.6084/m9.figshare.4541233
title: S2 Table Phyla data summary.xlsx

description: Summary of fecal bacterial abundance in dogs with MUO
DOI: 10.6084/m9.figshare.4541227
title: S1 Table Signalment, Prevotella and F prausnitizii.xlsx

description: Dataset showing relationship of signalment and fecal abundance of Prevotellacae and F prausnitzii
DOI: 10.6084/m9.figshare.4541188
title: Wild Type CA1 Automated Imaging Volume Measurements During sLTP

description: Volume measurements collected from CA1 dendritic spines before after uncaging. Data is described in Figure 4 of paper by Smirnov et al (2017) : Automated remote focusing, drift correction, and photostimulation to evaluate structural plasticity in dendritic spines
DOI: 10.6084/m9.figshare.4541188.v1
title: Wild Type CA1 Automated Imaging Volume Measurements During sLTP

description: Volume measurements collected from CA1 dendritic spines before after uncaging. Data is described in Figure 4 of paper by Smirnov et al (2017) : Automated remote focusing, drift correction, and photostimulation to evaluate structural plasticity in dendritic spines
DOI: 10.6084/m9.figshare.4541113
title: Validation of an established prognostic score after re-irradiation of recurrent glioma

description: <b>Background:</b> Re-irradiation (Re-RT) is offered widely in clinical routine, and has been established as a key element in the treatment of recurrent gliomas. At our center, generally re-resection is performed widely by an experienced neurosurgical team. Thus, Re-RT mostly offered to patients with macroscopic residuals or irresectable lesions, is applied later compared to other centers. Therefore, we sought to validate the Combs Prognostic Score developed in 2012 using our independent patient cohort. <b>Patients and methods:</b> We included 199 patients treated from 2002 until April 2016 for recurrent glioma at the Department of Radiation Oncology at the Klinikum Rechts der Isar, Munich. Different concepts of Re-RT were applied. <b>Results:</b> Median follow-up after Re-RT was 2.5 months. Median overall survival (OS) after Re-RT was 7.9 months for WHO IV gliomas, 11.3 months for WHO III gliomas, and 13.6 months for low-grade gliomas (WHO I/II). Univariate analyses confirmed the prognostic factors primary histology (p = 0.001), age (p = 0.002), and time between primary radiotherapy and Re-RT (p <b>Conclusion:</b> In our analysis, we validated the Combs Prognostic Score. Validation in this independent large patient cohort confirms the significance of the score for glioma recurrences. Thus, the role of the Combs Prognostic Score might be an essential component of future clinical decision making and patient stratification.
DOI: 10.6084/m9.figshare.4541032
title: Supplementary Material for: Mechanical Force-Induced Specific MicroRNA Expression in Human Periodontal Ligament Stem Cells

description: It remains unclear how the expression of microRNAs (miRNAs) in human periodontal ligament stem cells (PDLSCs) might respond to mechanical stretch. To investigate specific miRNA expression in stretched PDLSCs, we used a Flexcell® FX-5000™ tension system to achieve external mechanical stimulation. Then, a custom-designed microarray assay was performed to investigate and describe the genome-wide differential expression of miRNAs in normal and stretched PDLSCs. Finally, we implemented integrative miRNA target prediction and network analysis approaches to construct an interaction network of the key miRNAs and their putative targets. We found that stretching induced morphological changes and increased alkaline phosphatase (ALP) activity, runt-related transcription factor 2 (RUNX2), osteocalcin (OCN), and bone sialoprotein (BSP) expression in PDLSCs. The microarray data showed that 53 miRNAs were differentially expressed with stretching. With an interaction network, we examined the connections between 10 selected key miRNAs and their putative target genes, which were related to mechanical force. The results from the interaction network provided a basis for postulating the functional roles of miRNAs in PDLSCs.
DOI: 10.6084/m9.figshare.4541113.v1
title: Validation of an established prognostic score after re-irradiation of recurrent glioma

description: <b>Background:</b> Re-irradiation (Re-RT) is offered widely in clinical routine, and has been established as a key element in the treatment of recurrent gliomas. At our center, generally re-resection is performed widely by an experienced neurosurgical team. Thus, Re-RT mostly offered to patients with macroscopic residuals or irresectable lesions, is applied later compared to other centers. Therefore, we sought to validate the Combs Prognostic Score developed in 2012 using our independent patient cohort. <b>Patients and methods:</b> We included 199 patients treated from 2002 until April 2016 for recurrent glioma at the Department of Radiation Oncology at the Klinikum Rechts der Isar, Munich. Different concepts of Re-RT were applied. <b>Results:</b> Median follow-up after Re-RT was 2.5 months. Median overall survival (OS) after Re-RT was 7.9 months for WHO IV gliomas, 11.3 months for WHO III gliomas, and 13.6 months for low-grade gliomas (WHO I/II). Univariate analyses confirmed the prognostic factors primary histology (p = 0.001), age (p = 0.002), and time between primary radiotherapy and Re-RT (p <b>Conclusion:</b> In our analysis, we validated the Combs Prognostic Score. Validation in this independent large patient cohort confirms the significance of the score for glioma recurrences. Thus, the role of the Combs Prognostic Score might be an essential component of future clinical decision making and patient stratification.
DOI: 10.6084/m9.figshare.4541020
title: Supplementary Material for: Overall Response to First-Line Tyrosine Kinase Inhibitor and Second-Line Chemotherapy Is Predictive of Survival Outcome in Epidermal Growth Factor Receptor-Mutated Adenocarcinoma

description: <b><i>Background:</i></b> First-line epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are effective for the treatment of lung adenocarcinoma with an <i>EGFR</i>-sensitizing mutation, but resistance is inevitable. Chemotherapy is widely used in the second-line setting. The outcome following this treatment scheme has not been thoroughly evaluated. <b><i>Methods:</i></b> From 2007 to 2011, consecutive patients with mutated <i>EGFR</i> receiving first-line TKI and second-line chemotherapy were retrospectively reviewed. The overall response was categorized into double responder, single responder and double nonresponder. <b><i>Results:</i></b> Following this treatment scheme, baseline Eastern Cooperative Oncology Group (ECOG) performance status 0-1 (HR 0.60; 95% CI 0.37-0.98; p = 0.041) and double responder (HR 0.24; 95% CI 0.07-0.78; p = 0.018) were independent predictors of overall survival. Absence of pleural metastasis independently predicted the response to first-line TKI (OR 2.60; 95% CI 1.13-5.99; p = 0.025). In TKI responders, ECOG performance status 0-1 before chemotherapy (OR 4.95; 95% CI 1.15-21.28; p = 0.006), an exon 19 deletion (OR 4.74; 95% CI 1.30-17.21; p = 0.018) and progression-free survival (PFS) on first-line TKI (OR 1.02; 95% CI 1.01-1.09; p = 0.049) independently predicted the response to second-line chemotherapy. A moderate linear relationship (Pearson's r = 0.441; p = 0.001) existed between the PFS of this treatment scheme in TKI responders. <b><i>Conclusion:</i></b> The status of double responder to first-line TKI and second-line chemotherapy was predictive of improved survival in <i>EGFR</i>-mutated adenocarcinoma.
DOI: 10.6084/m9.figshare.4541014
title: Supplementary Material for: A New Method to Measure the Subpubic Arch Angle Using 3-D Ultrasound

description: <b><i>Objectives:</i></b> The aim of this study was to assess the reproducibility of both a new contrast-enhancing technique (Oblique View eXtended Imaging, OVIX; Samsung) and the recently reported 3-D multiplanar technique (MPT) in the measurement of the subpubic angle (SPA) among a group of women at term gestation. In addition, we aimed to study the intermethod agreement between the OVIX technique and MPT. <b><i>Methods:</i></b> We acquired a transperineal 3-D ultrasound volume from 155 women with a singleton uncomplicated term pregnancy before the onset of labor. Each 3-D dataset was analyzed by the MPT and OVIX algorithm. The angle formed by the lower edges of the pubic rami (SPA) was measured twice by an operator and once by another operator for each technique in order to assess intra- and interobserver reproducibility. Reproducibility and intermethod agreement were studied by means of the intraclass correlation coefficient (ICC) and Bland-Altman method. <b><i>Results:</i></b> SPA measurements performed with OVIX showed high intraobserver [ICC 0.912, 95% confidence interval (CI) 0.882-0.935] and good interobserver (ICC 0.791, 95% CI 0.724-0.844) agreement, while those measured with MPT showed moderate intraobserver (ICC 0.573, 95% CI 0.457-0.670) and good interobserver (ICC 0.640, 95% CI 0.537-0.724) agreement. Whereas the intermethod analysis showed good agreement between the MPT and the OVIX techniques (ICC 0.614, 95% CI 0.414-0.757), the SPA measured by MPT were significantly wider than those measured by OVIX (125 ± 12 vs. 120 ± 11°, p = 0.006). <b><i>Conclusions:</i></b> OVIX is a reliable technique for SPA measurement. MPT overestimates the SPA in comparison with OVIX. Further studies are needed to assess its clinical utility.
DOI: 10.6084/m9.figshare.4541020.v1
title: Supplementary Material for: Overall Response to First-Line Tyrosine Kinase Inhibitor and Second-Line Chemotherapy Is Predictive of Survival Outcome in Epidermal Growth Factor Receptor-Mutated Adenocarcinoma

description: <b><i>Background:</i></b> First-line epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are effective for the treatment of lung adenocarcinoma with an <i>EGFR</i>-sensitizing mutation, but resistance is inevitable. Chemotherapy is widely used in the second-line setting. The outcome following this treatment scheme has not been thoroughly evaluated. <b><i>Methods:</i></b> From 2007 to 2011, consecutive patients with mutated <i>EGFR</i> receiving first-line TKI and second-line chemotherapy were retrospectively reviewed. The overall response was categorized into double responder, single responder and double nonresponder. <b><i>Results:</i></b> Following this treatment scheme, baseline Eastern Cooperative Oncology Group (ECOG) performance status 0-1 (HR 0.60; 95% CI 0.37-0.98; p = 0.041) and double responder (HR 0.24; 95% CI 0.07-0.78; p = 0.018) were independent predictors of overall survival. Absence of pleural metastasis independently predicted the response to first-line TKI (OR 2.60; 95% CI 1.13-5.99; p = 0.025). In TKI responders, ECOG performance status 0-1 before chemotherapy (OR 4.95; 95% CI 1.15-21.28; p = 0.006), an exon 19 deletion (OR 4.74; 95% CI 1.30-17.21; p = 0.018) and progression-free survival (PFS) on first-line TKI (OR 1.02; 95% CI 1.01-1.09; p = 0.049) independently predicted the response to second-line chemotherapy. A moderate linear relationship (Pearson's r = 0.441; p = 0.001) existed between the PFS of this treatment scheme in TKI responders. <b><i>Conclusion:</i></b> The status of double responder to first-line TKI and second-line chemotherapy was predictive of improved survival in <i>EGFR</i>-mutated adenocarcinoma.
DOI: 10.6084/m9.figshare.4540981
title: Supplementary Material for: Stress Response to the Functional Magnetic Resonance Imaging Environment in Healthy Adults Relates to the Degree of Limbic Reactivity during Emotion Processing

description: <b><i>Background:</i></b> Imaging techniques are increasingly being used to examine the neural correlates of stress and emotion processing; however, relations between the primary stress hormone cortisol, the functional magnetic resonance imaging (fMRI) environment, and individual differences in response to emotional challenges are not yet well studied. The present study investigated whether cortisol activity prior to, and during, an fMRI scan may be related to neural processing of emotional information. <b><i>Methods:</i></b> Twenty-six healthy individuals (10 female) completed a facial emotion perception test during 3-tesla fMRI. <b><i>Results:</i></b> Prescan cortisol was significantly correlated with enhanced amygdala, hippocampal, and subgenual cingulate reactivity for facial recognition. Cortisol change from pre- to postscanning predicted a greater activation in the precuneus for both fearful and angry faces. A negative relationship between overall face accuracy and activation in limbic regions was observed. <b><i>Conclusion:</i></b> Individual differences in response to the fMRI environment might lead to a greater heterogeneity of brain activation in control samples, decreasing the power to detect differences between clinical and comparison groups.
DOI: 10.6084/m9.figshare.4540963
title: 6_23_2016 (IL 40)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4540960
title: Supplementary Material for: Dysfunctional Dopaminergic Neurones in Mouse Models of Huntington's Disease: A Role for SK3 Channels

description: <b><i>Background:</i></b> Huntington's disease (HD) is a late-onset fatal neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the gene coding for the protein huntingtin and is characterised by progressive motor, psychiatric and cognitive decline. We previously demonstrated that normal synaptic function in HD could be restored by application of dopamine receptor agonists, suggesting that changes in the release or bioavailability of dopamine may be a contributing factor to the disease process. <b><i>Objective:</i></b> In the present study, we examined the properties of midbrain dopaminergic neurones and dopamine release in presymptomatic and symptomatic transgenic HD mice. <b><i>Methods and Results:</i></b> Using intracellular sharp recordings and immunohistochemistry, we found that neuronal excitability was increased due to a loss of slow afterhyperpolarisation and that these changes were related to an apparent functional loss and abnormal distribution of SK3 channels (K<sub>Ca</sub>2.3 encoded by the <i>KCNN3</i> gene), a class of small-conductance calcium-activated potassium channels. Electrochemical detection of dopamine showed that this observation was associated with an enhanced dopamine release in presymptomatic transgenic mice and a drastic reduction in symptomatic animals. These changes occurred in the context of a progressive expansion in the CAG repeat number and nuclear localisation of mutant protein within the substantia nigra pars compacta. <b><i>Conclusions:</i></b> Dopaminergic neuronal dysfunction is a key early event in HD disease progression. The initial increase in dopamine release appears to be related to a loss of SK3 channel function, a protein containing a polyglutamine tract. Implications for polyglutamine-mediated sequestration of SK3 channels, dopamine-associated DNA damage and CAG expansion are discussed in the context of HD.
DOI: 10.6084/m9.figshare.4540981.v1
title: Supplementary Material for: Stress Response to the Functional Magnetic Resonance Imaging Environment in Healthy Adults Relates to the Degree of Limbic Reactivity during Emotion Processing

description: <b><i>Background:</i></b> Imaging techniques are increasingly being used to examine the neural correlates of stress and emotion processing; however, relations between the primary stress hormone cortisol, the functional magnetic resonance imaging (fMRI) environment, and individual differences in response to emotional challenges are not yet well studied. The present study investigated whether cortisol activity prior to, and during, an fMRI scan may be related to neural processing of emotional information. <b><i>Methods:</i></b> Twenty-six healthy individuals (10 female) completed a facial emotion perception test during 3-tesla fMRI. <b><i>Results:</i></b> Prescan cortisol was significantly correlated with enhanced amygdala, hippocampal, and subgenual cingulate reactivity for facial recognition. Cortisol change from pre- to postscanning predicted a greater activation in the precuneus for both fearful and angry faces. A negative relationship between overall face accuracy and activation in limbic regions was observed. <b><i>Conclusion:</i></b> Individual differences in response to the fMRI environment might lead to a greater heterogeneity of brain activation in control samples, decreasing the power to detect differences between clinical and comparison groups.
DOI: 10.6084/m9.figshare.4540960.v1
title: Supplementary Material for: Dysfunctional Dopaminergic Neurones in Mouse Models of Huntington's Disease: A Role for SK3 Channels

description: <b><i>Background:</i></b> Huntington's disease (HD) is a late-onset fatal neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the gene coding for the protein huntingtin and is characterised by progressive motor, psychiatric and cognitive decline. We previously demonstrated that normal synaptic function in HD could be restored by application of dopamine receptor agonists, suggesting that changes in the release or bioavailability of dopamine may be a contributing factor to the disease process. <b><i>Objective:</i></b> In the present study, we examined the properties of midbrain dopaminergic neurones and dopamine release in presymptomatic and symptomatic transgenic HD mice. <b><i>Methods and Results:</i></b> Using intracellular sharp recordings and immunohistochemistry, we found that neuronal excitability was increased due to a loss of slow afterhyperpolarisation and that these changes were related to an apparent functional loss and abnormal distribution of SK3 channels (K<sub>Ca</sub>2.3 encoded by the <i>KCNN3</i> gene), a class of small-conductance calcium-activated potassium channels. Electrochemical detection of dopamine showed that this observation was associated with an enhanced dopamine release in presymptomatic transgenic mice and a drastic reduction in symptomatic animals. These changes occurred in the context of a progressive expansion in the CAG repeat number and nuclear localisation of mutant protein within the substantia nigra pars compacta. <b><i>Conclusions:</i></b> Dopaminergic neuronal dysfunction is a key early event in HD disease progression. The initial increase in dopamine release appears to be related to a loss of SK3 channel function, a protein containing a polyglutamine tract. Implications for polyglutamine-mediated sequestration of SK3 channels, dopamine-associated DNA damage and CAG expansion are discussed in the context of HD.
DOI: 10.6084/m9.figshare.4540933
title: 6_22_2016 (IL 40/50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4540963.v1
title: 6_23_2016 (IL 40)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4540933.v1
title: 6_22_2016 (IL 40/50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.