cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10561059
title: Post-hypnotic safety suggestion improves stress coping with long-lasting effects

description: Effective coping with acute stress is important to promote mental health and to build stress resilience. Interventions improving stress coping usually require long training periods. In this study, we present a hypnosis-based intervention that produces long-term effects after a single hypnosis session. In that session, we established a post-hypnotic safety suggestion that participants can activate afterwards with a cue. We tested 60 participants in our study who all received the hypnosis session and a stress task. The safety group used the post-hypnotic safety cue during acute stress (Trier Social Stress Test, TSST). The control group used a neutral trigger instead. We measured subjective stress responses via self-reports and physiological stress responses via saliva and blood samples as well as heart rate. One week later, all participants filled in an online survey to measure long-term effects of the post-hypnotic safety suggestion. We found that participants using the post-hypnotic safety cue during the TSST reported significantly lower stress compared to the control group. The safety group also reported significantly fewer negative thoughts concerning their TSST performance than the control group during the stress recovery phase and one week later. All participants indicated that the post-hypnotic safety suggestion still worked one week after its establishment. Suggestibility did not affect the efficacy of the post-hypnotic safety suggestion. Our findings demonstrate that post-hypnotic safety suggestions improve stress coping with long-lasting effects, which makes it a promising intervention to promote mental health and establish stress resilience in just one hypnosis session.

The manuscript is published in Scientific Reports on February 12, 2024 and available here: https://doi.org/10.1038/s41598-024-54071-3
description: The German Research Council (DFG) funded this study with a grant to Dr. Barbara Schmidt (SCHM 3129/5-1).
DOI: 10.5281/zenodo.7829182
title: Post-hypnotic safety suggestion improves stress coping with long-lasting effects

description: Effective coping with acute stress is important to promote mental health and to build stress resilience. Interventions improving stress coping usually require long training periods. In this study, we present a hypnosis-based intervention that produces long-term effects after a single hypnosis session. In that session, we established a post-hypnotic safety suggestion that participants can activate afterwards with a cue. We tested 60 participants in our study who all received the hypnosis session and a stress task. The safety group used the post-hypnotic safety cue during acute stress (Trier Social Stress Test, TSST). The control group used a neutral trigger instead. We measured subjective stress responses via self-reports and physiological stress responses via saliva and blood samples as well as heart rate. One week later, all participants filled in an online survey to measure long-term effects of the post-hypnotic safety suggestion. We found that participants using the post-hypnotic safety cue during the TSST reported significantly lower stress compared to the control group. The safety group also reported significantly fewer negative thoughts concerning their TSST performance than the control group during the stress recovery phase and one week later. All participants indicated that the post-hypnotic safety suggestion still worked one week after its establishment. Suggestibility did not affect the efficacy of the post-hypnotic safety suggestion. Our findings demonstrate that post-hypnotic safety suggestions improve stress coping with long-lasting effects, which makes it a promising intervention to promote mental health and establish stress resilience in just one hypnosis session.

The manuscript is published in Scientific Reports on February 12, 2024 and available here: https://doi.org/10.1038/s41598-024-54071-3
description: The German Research Council (DFG) funded this study with a grant to Dr. Barbara Schmidt (SCHM 3129/5-1).
DOI: 10.48577/jpl.vljyyi
title: Estimation of the Heliocentric Momentum Enhancement from a Kinetic Impact: The Double Asteroid Redirection Test (DART) Mission

description: The NASA Double Asteroid Redirection Test (DART) has demonstrated the capability of successfully conducting kinetic impact-based asteroid deflection missions. The changes in the Didymos-Dimorphos mutual orbit as a result of the DART impact have been measured. To fully assess the heliocentric outcome of deflection missions, the heliocentric momentum enhancement parameter, β⊙, needs to be determined and disentangled from other non-gravitational phenomena such as the Yarkovsky effect. Here, we explore the measurability of β⊙ resulting from DART, which we estimate simultaneously with non-gravitational accelerations using a least squares filter. Results show that successful stellar occultation measurements of the Didymos system in the second half of 2024 in addition to the ones in the 2022-2023 campaigns can achieve a statistically significant estimate of β⊙, with an uncertainty slightly above 20% for an assumed β⊙ = 3. Adding additional occultation measurements and pseudo- range measurements from the Hera spacecraft operations at Didymos starting in 2027 decreases this relative uncertainty to under 6%. We find that pre-impact occultation observations combined with post-impact occultations would have yielded substantially higher signal-to-noise ratios on the heliocen- tric deflection. Additionally, pre-impact occultations would have also enabled a statistically significant β⊙ estimate using only one additional occultation in September 2023. Therefore, we conclude that future asteroid deflection missions would greatly benefit from both pre- and post-deflection occultation measurements to help assess the resulting orbital changes.
DOI: 10.48577/jpl.xbgobh
title: Orbital and physical characterization of asteroid Dimorphos following the DART impact

description: The Double Asteroid Redirection Test (DART) mission impacted Dimorphos, the satellite of binary near-Earth asteroid (65803) Didymos, on 2022 September 26 UTC. We estimate the changes in the orbital and physical properties of the system due to the impact using ground-based photometric and radar observations, as well as DART camera observations. We estimate that the DART impact instantaneously changed the along-track velocity of Dimorphos by −2.63 ± 0.06 mm s−1. Initially, after the impact, Dimorphos’s orbital period had changed by −32.7 minutes ± 16 s to 11.377 ± 0.004 h. We find that over the subsequent several weeks the orbital period changed by an additional 34±15 s, eventually stabilizing at 11.3674 ± 0.0004 h. The total change in the orbital period was −33.25 minutes ± 1.5 s. The post-impact orbit exhibits an apsidal precession rate of 6.7 ± 0.2 deg day−1. Under our model, this rate is driven by the oblateness parameter of Didymos, J2, as well as the spherical harmonics coefficients, C20 and C22, of Dimorphos’s gravity. Under the assumption that Dimorphos is a triaxial ellipsoid with a uniform density, its C20 and C22 estimates imply axial ratios, a/b and a/c, of about 1.3 and 1.6 respectively. Pre-impact images from DART indicate Dimorphos’s shape was close to that of an oblate spheroid, and thus our results indicate that the DART impact significantly altered the shape of Dimorphos.
DOI: 10.48577/jpl.utljnm
title: Environmental Justice and Lessons Learned from COVID-19 Outcomes – 1 Uncovering Hidden Patterns with Geometric Deep Learning and New NASA 2 Satellite Data

description: Irtually all aspects of our societal functioning – from food security to energy supply to healthcare – depend on the dynamics of environmental factors. Nevertheless, the social dimensions of weather and climate are noticeably less explored by the artificial intelligence community. Byharnessing the strength of geometric deep learning (GDL), we aim to investigate the pressing societal question the potential disproportional impacts of air quality on COVID-19 clinical severity. To quantify air pollution levels, here we use aerosol optical depth (AOD) records which measurethe reduction of the sunlight due to atmospheric haze, dust, and smoke. We also introduceunique and not yet broadly available NASA satellite records (NASAdat) on AOD, temperature andrelative humidity and discuss the utility of these new data for biosurveillance and climate justiceapplications, with a specific focus on COVID-19 in the States of Texas and Pennsylvania in USA.The results indicate that, in general, the poorer air quality tends to be associated with higherrates for clinical severity and, in case of Texas, this phenomenon particularly stands out in Texancounties characterized by higher socioeconomic vulnerability. This, in turn, raises a concern ofenvironmental injustice in these socio-economically disadvantaged communities. Furthermore,given that one of NASA’s recent long-term commitments is to address such inequitable burden ofenvironmental harm by expanding use of Earth science data such as NASAdat, this project is oneof the first steps toward developing a new platform integrating NASA’s satellite observations withDL tools for social good.
DOI: 10.48577/jpl.ngaffp
title: How to identify cell material in a single ice grain emitted from Enceladus or Europa

description: Icy moons like Enceladus, and perhaps Europa, appear to express material sourced from their subsurface oceans into space via plumes of ice grains and gas. Cassini’s Cosmic Dust Analyzer (CDA) revealed that Enceladus’ ocean is salty, hydrothermally active, and contains organic compounds. Only 1-3 % of Enceladus’ plume grains contain organic material in high concentrations, highlighting the importance of compositional analyses of individual grains compared to a bulk sample. Currently this is only possible via impact ionization mass spectrometry, as employed by CDA or Europa Clipper’s SUrface Dust Analyzer. Here we report experiments simulating the impact ionization mass spectra of ice grains containing one bacterial cell, or fractions thereof, as encountered by a spacecraft at flyby speeds of 4-6 km/s. Mass spectral signals characteristic of the bacteria are shown to be clearly identifiable by future impact ionization mass spectrometers, even if an ice grain contains much less than one cell.
DOI: 10.48577/jpl.yqdpmo
title: Optimized GNSS cal/val site selection for expanding InSAR viability in areas with low phase coherence: A case study for southern Louisiana

description: Interferometric Synthetic Aperture Radar (InSAR)techniques can be used to derive spatially dense “relative”measurements of vertical land motion (VLM), whereas GlobalNavigation Satellite System (GNSS) provides point-based“absolute” measurements of VLM. The combination of GNSS andInSAR observations can yield spatially dense VLM measurementsin an absolute reference frame. Additionally, GNSS observationscan be used to correct atmospheric noise in InSAR deformationmeasurements, and serve as a complementary measure to isolatedeep and shallow subsidence components. Given the increasingspatial and temporal coverage available from InSAR satellites,there is a need to establish calibration/validation (cal/val)networks that enable use of InSAR for measuring VLM incoherence-challenged areas such as many low-lying coastal lands.In this study, we provide a method for selection of sites for newGNSS installations such that the resulting GNSS network canbetter serve as tie points and validation for InSAR in areas wherelow coherence prevents high-fidelity phase unwrapping. Ourmethod is applied in a case study for expanding the existing GNSSnetwork in southern Louisiana, using abandoned oil well sites aspotential sites. Considering practical limitations, distributionamong various land classes, and following National GeodeticSurvey guidelines, our proposed GNSS network consists of 61 (45existing + 16 new) stations spread over a 50000 km2 area ofsouthern Louisiana.
DOI: 10.48577/jpl.hatulv
title: Seismically Detected Cratering on Mars: Enhanced Recent Impact Flux?

description: Seismic observations of impacts on Mars indicate a higher impact flux than previously measured. Using six confirmed seismic impact detections near the NASA InSight lander and two distant large impacts, we calculate appropriate scalings to compare these rates with lunar-based chronology models. We also update the impact rate from orbital observations using the most recent catalog of new craters on Mars. The snapshot of the current impact rate at Mars recorded seismically is higher than that found using orbital detections alone. The measured rates differ between a factor of two to ten, depending on the diameter, although the sample size of seismically detected impacts is small. The close timing of the two largest new impacts discovered on Mars in the last few decades indicates either a heightened impact rate, or a low-probability temporal coincidence, perhaps representing recent fragmentation of a parent body. We conclude that seismic methods of detecting current impacts offer a more complete dataset than orbital imaging.
DOI: 10.5281/zenodo.3378054
title: Critical Assessment of RNA-Seq Differential Expression

description: Warden and Wu Preprint: v1

In general, this primarily focuses on the following types of comparisons:



Cell line experiments with over-expression or knock-down to define a known causal gene, with processing starting with public reads.

Processed TCGA (The Cancer Genome Atlas) data for breast cancer (BRCA) to compare gene expression by immunohistochemistry status (ER/ESR1, PR/PGR, or HER2/ERBB2).


Differential expression methods include the following:



edgeR (GLM)

edgeR-robust (GLM)

edgeR (QL)

edgeR-robust (QL)

DESeq1

DESeq2

limma-voom

limma-trend (CPM)

limma-trend (FPKM/RPKM)

ANOVA (log2 FRPKM/RPKM)


The most common preprocessing strategies include STAR, TopHat2, and Salmon.  However, a limited amount of additional processing with HISAT2, kallisto, Bowtie2 (+eXpress), and Bowtie1 (+RSEM) is also provided.

Most STAR and TopHat2 alignments use htseq-count for quantification, as well as running cuffdiff (for single variable 2-group comparisons).  However, a limited amount of additional processing with featureCounts is also provided.

Most STAR and TopHat2 alignments start with the public forward reads, even if paired-end data was available.
description: While the analysis has to come as a secondary priority to other responsibilities, this data set can serve at least two purposes:
1) Provide an experimental public lab notebook / log for an on-going experiment:
https://sourceforge.net/projects/rnaseq-deg-methodlimit/files/LOG.txt
2) Provided an updated citation for RNA-Seq methods used for core support (at least for Charles Warden).
In the meantime, the best citation to use is probably the GitHub acknowledgements: https://github.com/cwarden45/RNAseq_templates/blob/master/TopHat_Workflow/README.md
description: For an earlier version of the templates for RNA-Seq analysis, acknowledgements were listed for labs in a subfolder of the GitHub repository.

So, we would like to provide similar acknowledgements for labs supported since that time (in a similar way).  Namely, we would also like to thank the following users that gave us permission to acknowledge these templates (or scripts similar to these templates) were used for analysis of their data: Ke Ma (with lab members Xuekai Xiong, Weini Li, and Tali Kiperman), Saul Priceman (with lab members Yukiko Yamaguchi, Hee Jun/Eric Lee, Anthony Park, and John Murad), Jose Enrique Montero Casimiro / Bart Roep (with Veronica Lifshitz and David Arribas-Layton), Rebecca Deegan (UNMC, with lab member Elizabeth Kosmacek), James Figarola (with lab member Jyotsana Singhal and collaborator Josh Tompkins), Linda Malkas (with lab member Robert Lingeman), and Stephen Forman / Christine Brown (with lab member Dongrui Wang).  There are also 5 internal collaborators with whom there was not clear confirmation for approval; however, this acknowledgement can be updated in the future.
DOI: 10.5281/zenodo.3378055
title: Critical Assessment of RNA-Seq Differential Expression

description: Warden and Wu Preprint: v1

In general, this primarily focuses on the following types of comparisons:



Cell line experiments with over-expression or knock-down to define a known causal gene, with processing starting with public reads.

Processed TCGA (The Cancer Genome Atlas) data for breast cancer (BRCA) to compare gene expression by immunohistochemistry status (ER/ESR1, PR/PGR, or HER2/ERBB2).


Differential expression methods include the following:



edgeR (GLM)

edgeR-robust (GLM)

edgeR (QL)

edgeR-robust (QL)

DESeq1

DESeq2

limma-voom

limma-trend (CPM)

limma-trend (FPKM/RPKM)

ANOVA (log2 FRPKM/RPKM)


The most common preprocessing strategies include STAR, TopHat2, and Salmon.  However, a limited amount of additional processing with HISAT2, kallisto, Bowtie2 (+eXpress), and Bowtie1 (+RSEM) is also provided.

Most STAR and TopHat2 alignments use htseq-count for quantification, as well as running cuffdiff (for single variable 2-group comparisons).  However, a limited amount of additional processing with featureCounts is also provided.

Most STAR and TopHat2 alignments start with the public forward reads, even if paired-end data was available.
description: While the analysis has to come as a secondary priority to other responsibilities, this data set can serve at least two purposes:
1) Provide an experimental public lab notebook / log for an on-going experiment:
https://sourceforge.net/projects/rnaseq-deg-methodlimit/files/LOG.txt
2) Provided an updated citation for RNA-Seq methods used for core support (at least for Charles Warden).
In the meantime, the best citation to use is probably the GitHub acknowledgements: https://github.com/cwarden45/RNAseq_templates/blob/master/TopHat_Workflow/README.md
description: For an earlier version of the templates for RNA-Seq analysis, acknowledgements were listed for labs in a subfolder of the GitHub repository.

So, we would like to provide similar acknowledgements for labs supported since that time (in a similar way).  Namely, we would also like to thank the following users that gave us permission to acknowledge these templates (or scripts similar to these templates) were used for analysis of their data: Ke Ma (with lab members Xuekai Xiong, Weini Li, and Tali Kiperman), Saul Priceman (with lab members Yukiko Yamaguchi, Hee Jun/Eric Lee, Anthony Park, and John Murad), Jose Enrique Montero Casimiro / Bart Roep (with Veronica Lifshitz and David Arribas-Layton), Rebecca Deegan (UNMC, with lab member Elizabeth Kosmacek), James Figarola (with lab member Jyotsana Singhal and collaborator Josh Tompkins), Linda Malkas (with lab member Robert Lingeman), and Stephen Forman / Christine Brown (with lab member Dongrui Wang).  There are also 5 internal collaborators with whom there was not clear confirmation for approval; however, this acknowledgement can be updated in the future.
DOI: 10.5281/zenodo.10652024
title: Data and Code for Silva and Halappanavar 2024

description: This is the code and data for Silva and Halappanavar, 2024. A paper submitted for publication titled "Graph Characterization of Higher Order Structure in Atmospheric Chemical Reaction Mechanisms"
DOI: 10.5281/zenodo.10652025
title: Data and Code for Silva and Halappanavar 2024

description: This is the code and data for Silva and Halappanavar, 2024. A paper submitted for publication titled "Graph Characterization of Higher Order Structure in Atmospheric Chemical Reaction Mechanisms"
DOI: 10.6084/m9.figshare.24887034
title: Low-risk penicillin allergy delabeling: a scoping review of direct oral challenge practice, implementation, and multi-disciplinary approaches

description: Penicillin allergy is common, and there is increased clinician interest in direct oral challenge (DOC) as a testing strategy for low-risk penicillin allergy. To aid wider implementation of DOC, consensus definitions of low-risk penicillin allergy phenotypes, and standardized approaches to assessment, DOC procedures, and evaluation, are required. This review systematically reviews studies that have utilized penicillin DOC in healthcare settings to identify heterogeneity in implementation approaches and synthesize low-risk definitions, procedures, and evaluation. Opportunity exists to standardize penicillin DOC procedures in patients with a low-risk penicillin allergy to optimize antimicrobial prescribing and reduce the burden of penicillin allergy. Standardizing the definitions of ‘low-risk’ and ‘positive challenge,’ and improving the evaluation of patient safety, alongside the development of a unified approach to the structure of undertaking an oral challenge, is likely to increase uptake and confidence among non-allergist clinicians.
DOI: 10.6084/m9.figshare.24887034.v1
title: Low-risk penicillin allergy delabeling: a scoping review of direct oral challenge practice, implementation, and multi-disciplinary approaches

description: Penicillin allergy is common, and there is increased clinician interest in direct oral challenge (DOC) as a testing strategy for low-risk penicillin allergy. To aid wider implementation of DOC, consensus definitions of low-risk penicillin allergy phenotypes, and standardized approaches to assessment, DOC procedures, and evaluation, are required. This review systematically reviews studies that have utilized penicillin DOC in healthcare settings to identify heterogeneity in implementation approaches and synthesize low-risk definitions, procedures, and evaluation. Opportunity exists to standardize penicillin DOC procedures in patients with a low-risk penicillin allergy to optimize antimicrobial prescribing and reduce the burden of penicillin allergy. Standardizing the definitions of ‘low-risk’ and ‘positive challenge,’ and improving the evaluation of patient safety, alongside the development of a unified approach to the structure of undertaking an oral challenge, is likely to increase uptake and confidence among non-allergist clinicians.
DOI: 10.6084/m9.figshare.25111542
title: Carbapenem-resistant <i>Klebsiella pneumoniae</i>: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge

description: <i>Klebsiella pneumoniae</i> is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in <i>K. pneumoniae</i> has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant <i>K. pneumoniae</i> (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids. Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in <i>K. pneumoniae</i>. CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.