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Article ; Online: Newborns and Children in War and Terror.

Saugstad, Ola Didrik / Modi, Neena / Moretti, Corrado / Obladen, Michael / Vento, Maximo / Speer, Christian P

2023 Volume 121, Issue 2, Page(s) 137–140

MeSH term(s)	Child ; Humans ; Infant, Newborn ; Armed Conflicts
Language	English
Publishing date	2023-12-12
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2266911-5
ISSN	1661-7819 ; 1661-7800
ISSN (online)	1661-7819
ISSN	1661-7800
DOI	10.1159/000535401
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Zs.A 391: Show issues

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Book ; Online: LLM-Assisted Content Analysis

Chew, Robert / Bollenbacher, John / Wenger, Michael / Speer, Jessica / Kim, Annice

Using Large Language Models to Support Deductive Coding

2023

Abstract: Deductive coding is a widely used qualitative research method for determining the prevalence of themes across documents. While useful, deductive coding is often burdensome and time consuming since it requires researchers to read, interpret, and reliably ... ...

Abstract	Deductive coding is a widely used qualitative research method for determining the prevalence of themes across documents. While useful, deductive coding is often burdensome and time consuming since it requires researchers to read, interpret, and reliably categorize a large body of unstructured text documents. Large language models (LLMs), like ChatGPT, are a class of quickly evolving AI tools that can perform a range of natural language processing and reasoning tasks. In this study, we explore the use of LLMs to reduce the time it takes for deductive coding while retaining the flexibility of a traditional content analysis. We outline the proposed approach, called LLM-assisted content analysis (LACA), along with an in-depth case study using GPT-3.5 for LACA on a publicly available deductive coding data set. Additionally, we conduct an empirical benchmark using LACA on 4 publicly available data sets to assess the broader question of how well GPT-3.5 performs across a range of deductive coding tasks. Overall, we find that GPT-3.5 can often perform deductive coding at levels of agreement comparable to human coders. Additionally, we demonstrate that LACA can help refine prompts for deductive coding, identify codes for which an LLM is randomly guessing, and help assess when to use LLMs vs. human coders for deductive coding. We conclude with several implications for future practice of deductive coding and related research methods.
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence ; Computer Science - Machine Learning ; Statistics - Applications
Publishing date	2023-06-23
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Barbecue conditions affect contents of oxygenated and non-oxygenated polycyclic aromatic hydrocarbons in meat and non-meat patties.

Zastrow, Lisa / Judas, Michael / Speer, Karl / Schwind, Karl-Heinz / Jira, Wolfgang

Food chemistry: X

2022 Volume 14, Page(s) 100351

Abstract: The contents of eight oxygenated polycyclic aromatic hydrocarbons (OPAHs; anthracene-9,10-dione, benzo[ ...

Abstract	The contents of eight oxygenated polycyclic aromatic hydrocarbons (OPAHs; anthracene-9,10-dione, benzo[
Language	English
Publishing date	2022-05-27
Publishing country	Netherlands
Document type	Journal Article
ISSN	2590-1575
ISSN (online)	2590-1575
DOI	10.1016/j.fochx.2022.100351
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Antarctic Peninsula warming triggers enhanced basal melt rates throughout West Antarctica.

Flexas, M Mar / Thompson, Andrew F / Schodlok, Michael P / Zhang, Hong / Speer, Kevin

Science advances

2022 Volume 8, Issue 32, Page(s) eabj9134

Abstract: The observed acceleration of ice shelf basal melt rates throughout West Antarctica could destabilize continental ice sheets and markedly increase global sea level. Explanations for decadal-scale melt intensification have focused on processes local to ... ...

Abstract	The observed acceleration of ice shelf basal melt rates throughout West Antarctica could destabilize continental ice sheets and markedly increase global sea level. Explanations for decadal-scale melt intensification have focused on processes local to shelf seas surrounding the ice shelves. A suite of process-based model experiments, guided by CMIP6 forcing scenarios, show that freshwater forcing from the Antarctic Peninsula, propagated between marginal seas by a coastal boundary current, causes enhanced melting throughout West Antarctica. The freshwater anomaly stratifies the ocean in front of the ice shelves and modifies vertical and lateral heat fluxes, enhancing heat transport into ice shelf cavities and increasing basal melt. Increased glacial runoff at the Antarctic Peninsula, one of the first signatures of a warming climate in Antarctica, emerges as a key trigger for increased ice shelf melt rates in the Amundsen and Bellingshausen Seas.
Language	English
Publishing date	2022-08-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.abj9134
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Imbalanced Inflammatory Responses in Preterm and Term Cord Blood Monocytes and Expansion of the CD14

Glaser, Kirsten / Kern, David / Speer, Christian P / Schlegel, Nicolas / Schwab, Michael / Thome, Ulrich H / Härtel, Christoph / Wright, Clyde J

International journal of molecular sciences

2023 Volume 24, Issue 5

Abstract: Developmentally regulated features of innate immunity are thought to place preterm and term infants at risk of infection and inflammation-related morbidity. Underlying mechanisms are incompletely understood. Differences in monocyte function including ... ...

Abstract	Developmentally regulated features of innate immunity are thought to place preterm and term infants at risk of infection and inflammation-related morbidity. Underlying mechanisms are incompletely understood. Differences in monocyte function including toll-like receptor (TLR) expression and signaling have been discussed. Some studies point to generally impaired TLR signaling, others to differences in individual pathways. In the present study, we assessed mRNA and protein expression of pro- and anti-inflammatory cytokines in preterm and term cord blood (CB) monocytes compared with adult controls stimulated ex vivo with Pam3CSK4, zymosan, polyinosinic:polycytidylic acid, lipopolysaccharide, flagellin, and CpG oligonucleotide, which activate the TLR1/2, TLR2/6, TLR3, TLR4, TLR5, and TLR9 pathways, respectively. In parallel, frequencies of monocyte subsets, stimulus-driven TLR expression, and phosphorylation of TLR-associated signaling molecules were analyzed. Independent of stimulus, pro-inflammatory responses of term CB monocytes equaled adult controls. The same held true for preterm CB monocytes-except for lower IL-1β levels. In contrast, CB monocytes released lower amounts of anti-inflammatory IL-10 and IL-1ra, resulting in higher ratios of pro-inflammatory to anti-inflammatory cytokines. Phosphorylation of p65, p38, and ERK1/2 correlated with adult controls. However, stimulated CB samples stood out with higher frequencies of intermediate monocytes (CD14
MeSH term(s)	Adult ; Infant, Newborn ; Humans ; Monocytes/metabolism ; Toll-Like Receptor 4/metabolism ; Lipopolysaccharides ; Toll-Like Receptor 1/metabolism ; Fetal Blood/metabolism ; Zymosan ; Toll-Like Receptors/metabolism ; Cytokines/metabolism ; Lipopolysaccharide Receptors/metabolism
Chemical Substances	Toll-Like Receptor 4 ; Lipopolysaccharides ; Toll-Like Receptor 1 ; Zymosan (9010-72-4) ; Toll-Like Receptors ; Cytokines ; Lipopolysaccharide Receptors
Language	English
Publishing date	2023-03-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24054919
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Pneumopericardium in the neonate: a case report.

Kataria-Hale, Jasmeet / Fernandes, Caraciolo J / Speer, Michael E

Perfusion

2019 Volume 35, Issue 4, Page(s) 360–362

Abstract: A term infant with cardiorespiratory failure treated with veno-venous extracorporeal membrane oxygenation developed pneumopericardium with cardiac tamponade while on the extracorporeal membrane oxygenation circuit. The patient was converted to veno- ... ...

Abstract	A term infant with cardiorespiratory failure treated with veno-venous extracorporeal membrane oxygenation developed pneumopericardium with cardiac tamponade while on the extracorporeal membrane oxygenation circuit. The patient was converted to veno-arterial extracorporeal membrane oxygenation and managed conservatively with spontaneous resolution of the air leak.
MeSH term(s)	Extracorporeal Membrane Oxygenation/methods ; Humans ; Infant, Newborn ; Male ; Pneumopericardium/diagnosis ; Pneumopericardium/pathology
Language	English
Publishing date	2019-08-15
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	645038-6
ISSN	1477-111X ; 0267-6591
ISSN (online)	1477-111X
ISSN	0267-6591
DOI	10.1177/0267659119868916
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 2424: Show issues

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Article ; Online: Respiratory syncytial virus pathophysiology and affect of palivizumab in special populations: cystic fibrosis and immunosuppression.

Speer, Michael E

The journal of pediatric pharmacology and therapeutics : JPPT : the official journal of PPAG

2011 Volume 16, Issue 2, Page(s) 74–76

Language	English
Publishing date	2011-11-12
Publishing country	United States
Document type	Journal Article
ISSN	2331-348X
ISSN (online)	2331-348X
DOI	10.5863/1551-6776-16.2.74
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Simultaneous determination of pesticides, mycotoxins, and metabolites as well as other contaminants in cereals by LC-LC-MS/MS.

Kresse, Michael / Drinda, Heike / Romanotto, Anna / Speer, Karl

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

2019 Volume 1117, Page(s) 86–102

Abstract: A 2D LC-MS/MS method for the simultaneous determination of 350 pesticides, 16 mycotoxins as well as the growth regulators Chlormequat and Mepiquat was developed. The method is applicable to cereals and products thereof. Attention should be paid to the ... ...

Abstract	A 2D LC-MS/MS method for the simultaneous determination of 350 pesticides, 16 mycotoxins as well as the growth regulators Chlormequat and Mepiquat was developed. The method is applicable to cereals and products thereof. Attention should be paid to the simultaneous analysis of the cereal-relevant mycotoxins aflatoxin B1, B2, G1 and G2, ochratoxin A, deoxynivalenol and zearalenone. Moreover, the tropane alkaloids atropine/scopolamine could be integrated into the final method. The samples were extracted with a mixture of acetonitrile/water (80:20), diluted with acetonitrile and injected into an LC-LC-MS/MS system. There were no further manual clean-up steps. The automatic online clean-up took place during the HILIC-separation in the first dimension (YMC-Pack Diol; 2.1 × 100 mm; 5 μm, 120 Å). Here, polar matrix compounds were retained, while the majority of the analyte scope eluted in a fraction at the beginning of the analytical run. This fraction was transferred to the second dimension by a packed loop interface (Agilent Zorbax SB-C8; 4.6 × 12.5 mm; 5 μm; 80 Å). On the second column (Phenomenex Synergi Fusion RP C18; 2 × 100 mm; 2.5 μm; 100 Å), the majority of the scope was separated by a typical RP-gradient. Only some of the polar pesticides could not be transferred to the second column. They eluted directly after the transfer step from the HILIC-column to the MS/MS. The final method was sensitive enough to meet all the regulated maximum levels for pesticides in cereals according to EU Regulation 396/2005 and those for contaminants according to EU Regulation 1881/2006. Above all, the method was so robust and accurate that nearly 90% of the pesticides and all the tested mycotoxins, growth regulators and tropane alkaloids fulfilled the validation criteria of the SANTE guideline document, although the demanding criteria are only applicable to pesticides. For the verification, eight proficiency tests were passed successfully: three for the pesticide analysis, three for the mycotoxin analysis, and two for the analysis of the tropane alkaloids. In addition to the already mentioned contaminants, the six most important ergot alkaloids (e.g. ergotamine/ergotaminine) and two modified mycotoxins (deoxynivalenol-3-glucoside and zearalenone-sulfate, also known as masked mycotoxins) were detected during the routine analysis of rye and corn samples.
MeSH term(s)	Chromatography, Liquid/methods ; Edible Grain/chemistry ; Food Contamination/analysis ; Limit of Detection ; Linear Models ; Mycotoxins/analysis ; Pesticide Residues/analysis ; Reproducibility of Results ; Tandem Mass Spectrometry/methods
Chemical Substances	Mycotoxins ; Pesticide Residues
Language	English
Publishing date	2019-04-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1180823-8
ISSN	1873-376X ; 0378-4347 ; 1570-0232 ; 1387-2273
ISSN (online)	1873-376X
ISSN	0378-4347 ; 1570-0232 ; 1387-2273
DOI	10.1016/j.jchromb.2019.04.013
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 813: Show issues

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Article ; Online: Rapid 3D-STORM imaging of diverse molecular targets in tissue.

Albrecht, Nicholas E / Jiang, Danye / Akhanov, Viktor / Hobson, Robert / Speer, Colenso M / Robichaux, Michael A / Samuel, Melanie A

Cell reports methods

2022 Volume 2, Issue 7, Page(s) 100253

Abstract: Fine-scale molecular architecture is critical for nervous system and other biological functions. Methods to visualize these nanoscale structures would benefit from enhanced accessibility, throughput, and tissue compatibility. Here, we report RAIN-STORM, ... ...

Abstract	Fine-scale molecular architecture is critical for nervous system and other biological functions. Methods to visualize these nanoscale structures would benefit from enhanced accessibility, throughput, and tissue compatibility. Here, we report RAIN-STORM, a rapid and scalable nanoscopic imaging optimization approach that improves three-dimensional visualization for subcellular targets in tissue at depth. RAIN-STORM uses conventional tissue samples and readily available reagents and is suitable for commercial instrumentation. To illustrate the efficacy of RAIN-STORM, we utilized the retina. We show that RAIN-STORM imaging is versatile and provide 3D nanoscopic data for over 20 synapse, neuron, glia, and vasculature targets. Sample preparation is also rapid, with a 1-day turnaround from tissue to image, and parameters are suitable for multiple tissue sources. Finally, we show that this method can be applied to clinical samples to reveal nanoscale features of human cells and synapses. RAIN-STORM thus paves the way for high-throughput studies of nanoscopic targets in tissue.
MeSH term(s)	Humans ; Microscopy, Fluorescence ; Imaging, Three-Dimensional ; Neurons ; Neuroglia ; Synapses
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2667-2375
ISSN (online)	2667-2375
DOI	10.1016/j.crmeth.2022.100253
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Imbalanced Inflammatory Responses in Preterm and Term Cord Blood Monocytes and Expansion of the CD14 + CD16 + Subset upon Toll-like Receptor Stimulation

Kirsten Glaser / David Kern / Christian P. Speer / Nicolas Schlegel / Michael Schwab / Ulrich H. Thome / Christoph Härtel / Clyde J. Wright

International Journal of Molecular Sciences, Vol 24, Iss 4919, p

2023 Volume 4919

Abstract	Developmentally regulated features of innate immunity are thought to place preterm and term infants at risk of infection and inflammation-related morbidity. Underlying mechanisms are incompletely understood. Differences in monocyte function including toll-like receptor (TLR) expression and signaling have been discussed. Some studies point to generally impaired TLR signaling, others to differences in individual pathways. In the present study, we assessed mRNA and protein expression of pro- and anti-inflammatory cytokines in preterm and term cord blood (CB) monocytes compared with adult controls stimulated ex vivo with Pam3CSK4, zymosan, polyinosinic:polycytidylic acid, lipopolysaccharide, flagellin, and CpG oligonucleotide, which activate the TLR1/2, TLR2/6, TLR3, TLR4, TLR5, and TLR9 pathways, respectively. In parallel, frequencies of monocyte subsets, stimulus-driven TLR expression, and phosphorylation of TLR-associated signaling molecules were analyzed. Independent of stimulus, pro-inflammatory responses of term CB monocytes equaled adult controls. The same held true for preterm CB monocytes—except for lower IL-1β levels. In contrast, CB monocytes released lower amounts of anti-inflammatory IL-10 and IL-1ra, resulting in higher ratios of pro-inflammatory to anti-inflammatory cytokines. Phosphorylation of p65, p38, and ERK1/2 correlated with adult controls. However, stimulated CB samples stood out with higher frequencies of intermediate monocytes (CD14 + CD16 + ). Both pro-inflammatory net effect and expansion of the intermediate subset were most pronounced upon stimulation with Pam3CSK4 (TLR1/2), zymosan (TR2/6), and lipopolysaccharide (TLR4). Our data demonstrate robust pro-inflammatory and yet attenuated anti-inflammatory responses in preterm and term CB monocytes, along with imbalanced cytokine ratios. Intermediate monocytes, a subset ascribed pro-inflammatory features, might participate in this inflammatory state.
Keywords	neonatal immunology ; inflammation ; preterm infants ; monocytes ; cord blood ; monocyte subsets ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	610
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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