Search

We present a parallel combination of existing, well-known and robust software used in modelling the neotectonics of planetary lithosphere, which we call ShellSet. An added parallel framework allows multiple models to be run at the same time with varied input parameters. Additionally, we have included a grid search option to automatically generate models within a given parameter space. ShellSet offers significant advantages over the original programs through its simplicity, efficiency and speed. We demonstrate the performance improvement obtained by ShellSet's parallel framework by presenting timing and speedup information for a parallel grid search, varying the number of processes and models, on both a typical computer and a high-performance computing cluster node. A possible use case for ShellSet is shown using two examples in which we improve on an existing global model. In the first example we improve the model using the same data, and in the second example we further improve the model through the addition of a new scoring dataset. The necessary ShellSet program version along with all the required input and post-processing files needed to recreate the results presented in this article are available at https://doi.org/10.5281/zenodo.7986808 (May et al., 2023).

Spaceborne lidar provides a unique opportunity to supplement the field plot measurements of national forest inventories (NFIs) by providing dense measurements of vertical canopy structure. For full waveform instruments such as the Global Ecosystem Dynamics Investigation (GEDI), measurements take the form of reflected energy as a function of height within an observed footprint. Many forest attributes cannot be directly computed from the waveforms, and thus statistical models relating the measurements to target attributes must be trained using field plot data. Because the discrete footprint samples produced by spaceborne lidar instruments have little chance of collocation with pre-existing field plots, model calibration remains a primary challenge. We leveraged the density and spatial correlation of GEDI observations to make predictions of the cumulative waveform over 326,787 NFI plots distributed across the contiguous United States. The predictions yield probability distributions, giving not only a predicted waveform but quantification of prediction uncertainty. The product of this work is a data set comprised of the NFI plots paired with the predictive waveform distributions. The predicted waveforms and their uncertainties can be used to train models with “error-in-variables” techniques that account for and filter the uncertainty in the predicted waveforms. This data set and the corresponding techniques allow statistically rigorous model training without requirements of collocation, yielding downstream forest attribute predictions that are consistent with NFI measurements and estimates. We demonstrate the data set by training a model for forest above ground biomass density (AGBD) and then use the model to produce a spatially complete 1 km map of AGBD for the contiguous United States. We further compare our AGBD predictions to US NFI estimates at a 64,000 hectare scale, showing the increase in precision to be proportional to the collection of almost 500,000 additional NFI plots across forested regions of CONUS.

Purpose: In lung squamous cell carcinoma (LUSC), Black patients show significantly higher incidence and lower overall survival than White patients. Although socioeconomic factors likely contribute to this survival disparity, genomic factors have yet to be elucidated in LUSC., Methods: Using 416 LUSC tumor samples in the Cancer Genome Atlas (TCGA), we assessed genomic and transcriptomic profiles by ancestry. We replicated our analyses in pan-cancer data from TCGA, the American Association of Cancer Research (AACR) Genomics Evidence Neoplasia Information Exchange (GENIE), and Columbia University Medical Center., Results: We found increased MYC amplification, LUSC-specific MYC enhancer amplification, and chromosome arm 8q (chr8q) gain to be significantly associated with genetic AFR (African) ancestry in LUSC in TCGA. Furthermore, expression of MYC target genes was significantly enriched in AFR samples. Local ancestry analysis identified correlation of chr8q gain with AFR ancestry at the MYC locus in TCGA. We also found a significant correlation between chr8q and AFR ancestry in multiple cancer types and pan-cancer in TCGA. Similarly, in a pan-cancer subset of AACR GENIE data, we found a significant correlation between chr8q gain and race., Conclusion: Together, our data suggest that ancestry may influence amplification of not only MYC but also its enhancer in LUSC. They also suggest a role for genetic ancestry in chr8q aneuploidy in cancer. These studies further define and expand patients who may benefit from future anti- MYC therapeutic approaches.

Background: Mentorship is the foundation for training and career development. However, only about half of interventional radiology (IR) residency programs in the United States have a formal mentorship program at their institution. A new tiered mentorship program was introduced at our institution., Methods: A structured mentorship program was created at our institution in 2020 for IR residents to pair 1-2 faculty advisors with a group of residents, one from each PGY class, based on personal interests and career paths. A quality improvement survey with Likert scale format (1-5) was sent to IR residents and faculty members., Results: Responses were recorded from 11 IR residents in addition to all 6 IR faculty mentors. IR respondents reported satisfaction with feeling more assimilated in the department and all would recommend the current mentorship model to other institutions. Most respondents agreed the program made them comfortable conducting effective mentorship relationships as an attending and that the tiered structured of being mentee and mentor simultaneously was beneficial. Both IR residents and faculty agreed that the program helped prevent burnout., Conclusions: The tiered mentorship model has had a positive impact on the IR program by providing structured mentoring and longitudinal relationships. The most notable benefits for IR residents is the early integration into the program, sustained mentorships relationships, and the prevention of burnout. Similar models can help other programs establish structured faculty and peer mentorship for residents early in training., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Ectopic pregnancies are one of the most common causes of obstetric mortality worldwide. Interstitial ectopic pregnancies, defined as an extracavitary pregnancy within the portion of the Fallopian tube that transverses the myometrium, have reported mortality rates approximately seven times higher than all types of ectopic pregnancy combined. In contrast, intracavitary eccentric gestations, often labeled as "cornual" or "angular" pregnancies, have reportedly high rates of live birth. Unfortunately, the terms "interstitial," "cornual," and "angular" have long been used with varying diagnostic criteria and often interchangeably to describe a pregnancy near the uterotubal junction. The inconsistency in nomenclature and lack of clear diagnostic criteria to distinguish among these pregnancies has resulted in a paucity of data to provide accurate prognostic information and guide appropriate management. This review article aims to provide historical context for the terms "interstitial," "cornual," and "angular;" discuss previous and more recent innovations of diagnostic methods; and provide recommendations for concise terminology and inform management., (© 2024. The Author(s), under exclusive licence to Society for Reproductive Investigation.)

Background: Astragalus membranaceus (AM) shows potential therapeutic benefits for managing diabetic kidney disease (DKD), a leading cause of kidney failure with no cure. However, its comprehensive effects on renal outcomes and plausible mechanisms remain unclear., Purpose: This systematic review and meta-analysis aimed to synthesize the effects and mechanisms of AM on renal outcomes in DKD animal models., Methods: Seven electronic databases were searched for animal studies until September 2023. Risk of bias was assessed based on SYRCLE's Risk of Bias tool. Standardized mean difference (SMD) or mean difference (MD) were estimated for the effects of AM on serum creatinine (SCr), blood urea nitrogen (BUN), albuminuria, histological changes, oxidative stress, inflammation, fibrosis and glucolipids. Effects were pooled using random-effects models. Heterogeneity was presented as I 2 . Subgroup analysis investigated treatment- and animal-related factors for renal outcomes. Publication bias was assessed using funnel plots and Egger's test. Sensitivity analysis was performed to assess the results' robustness. RevMan 5.3 and Stata MP 15 software were used for statistical analysis., Results: Forty studies involving 1543 animals were identified for analysis. AM treatment significantly decreased SCr (MD = -19.12 μmol/l, 95 % CI: -25.02 to -13.23), BUN (MD = -6.72 mmol/l, 95 % CI: -9.32 to -4.12), urinary albumin excretion rate (SMD = -2.74, 95 % CI: -3.57, -1.90), histological changes (SMD = -2.25, 95 % CI: -3.19 to -1.32). AM treatment significantly improved anti-oxidative stress expression (SMD = 1.69, 95 % CI: 0.97 to 2.41), and decreased inflammation biomarkers (SMD = -3.58, 95 % CI: -5.21 to -1.95). AM treatment also decreased fibrosis markers (i.e. TGF-β1, CTGF, collagen IV, Wnt4 and β-catenin) and increased anti-fibrosis marker BMP-7. Blood glucose, lipids and kidney size were also improved compared with the DM control group., Conclusion: AM could improve renal outcomes and alleviate injury through multiple signaling pathways. This indicates AM may be an option to consider for the development of future DKD therapeutics., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier GmbH.)

Background: There is increasing global evidence on the impact of advanced nursing and midwifery practitioners, and Kenya's healthcare system has an excellent opportunity to develop scopes of practice and other regulatory frameworks for the integration of these roles., Objective: The primary purpose of this gap analysis was to explore the existing evidence on opportunities and threats toward the integration of the advanced practice nursing (APN) and advanced practice midwifery (APM) roles in Kenya's healthcare system., Methods: The study team conducted a structured electronic database search of PubMed, CINAHL, Scopus, EBSCOhost Academic Search Complete, and PsycINFO to retrieve articles and credible websites for reports highlighting the opportunities and threats toward the integration of the APN and APM roles in Kenya's healthcare systems. The retrieved articles were screened for relevance and synthesized for reporting using the traditional literature review approach., Results: The Kenya Health Policy Framework 2014-2030, growing population needs, and implementation of universal health coverage provide an opportunity to harness and leverage advanced practice roles in nursing and midwifery. There is also momentum to develop advanced practice because of strategic alliances and global evidence showing the contributions and quality of services offered by advanced practice nurses and advanced practice midwives. However, lack of financial support, structural challenges, and lack of national policies, regulations, and legislation continue to obstruct progress., Conclusion and Implications for Nursing Policy: Developing scopes of practice for APN and APM in Kenya will benefit the professions, the country's healthcare delivery system, and the population. Achieving universal health coverage depends on a health workforce trained and practicing at optimal levels in tandem with education and training to deliver quality care., (© 2024 The Authors. International Nursing Review published by John Wiley & Sons Ltd on behalf of International Council of Nurses.)

Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting changes to normal biology. A disease reaction is defined as an aberrant reaction in which a variant protein participates. A disease pathway is defined as a pathway that contains a disease reaction. Annotation of disease variants as participants of disease reactions and disease pathways can provide a standardized overview of molecular phenotypes of pathogenic variants that is amenable to computational mining and mathematical modeling. Reactome (https://reactome.org/), an open source, manually curated, peer-reviewed database of human biological pathways, in addition to providing annotations for >11 000 unique human proteins in the context of ∼15 000 wild-type reactions within more than 2000 wild-type pathways, also provides annotations for >4000 disease variants of close to 400 genes as participants of ∼800 disease reactions in the context of ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, described in wild-type reactions and pathways, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Reactome's data model enables mapping of disease variant datasets to specific disease reactions within disease pathways, providing a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity. Database URL: https://reactome.org/., (© The Author(s) 2024. Published by Oxford University Press.)

Background: Health advances due to developments in genomic medicine are unequally experienced in the USA; racial differences in the uptake of genetic testing are one factor in this disparity. In collaboration with Black patients and diverse health care providers, we are developing a patient-centered video intervention to increase cancer genetic testing among eligible Black Americans. The objective of the pilot work is to explore the acceptability of and support for the intervention and key content components., Methods: In order to create a patient-centered video intervention prototype, we conducted a targeted, secondary analysis of 47 coded transcripts from video-taped qualitative interviews with people with a known genetic or inherited cancer risk. The review focused on decision-making, testing experiences, and perceived value of genetic testing. We subsequently generated a 15-min video montage of content from 9 diverse (age, gender, race) participants. We used the prototype video as prompt material for semi-structured interviews with 10 Black patients who had undergone genetic testing in the last 2 years and 10 racially diverse providers (genetic counselors, a nurse, and medical oncologists) who provide management recommendations for high-risk patients. Interviews sought to understand the acceptability of a video intervention to enhance informed decision-making by Black patients and key elements for intervention efficacy., Results: Study participants were generally positive about the prototype video and provided guidance for intervention development. Interviewed patients prioritized perceived authenticity and relatability of video participants. The presentation of patients' perspectives on testing, their experiences of testing, and the benefits of having test results were all seen as useful. The benefits of testing for self and family were identified as important considerations. Privacy concerns and science skepticism were identified as germane issues, with guidance to present barriers to testing alongside possible solutions. The inclusion of clinicians was seen as potentially useful but with caution that clinicians are not universally trusted., Conclusions: Study findings provided critical input for the creation of a professionally produced, tailored intervention video for a randomized clinical trial with Black Americans to evaluate the influence on uptake of genetic testing. The interviews suggest the acceptability and potential utility of an authentic, realistic, and tailored, patient-centered video intervention to increase consideration and uptake of genetic testing., (© 2024. The Author(s).)

The continuous rise in bacterial infections and antibiotic resistance is the driving force behind the search for new antibacterial agents with novel modes of action. Antimicrobial peptides (AMPs) have recently gained attention as promising antibiotic agents with the potential to treat drug-resistant infections. Several AMPs have shown a lower propensity towards developing resistance compared to conventional antibiotics. However, these peptides, especially acyldepsipeptides (ADEPs) present with unfavorable pharmacokinetic properties, such as high toxicity and low bioavailability. Different ways to improve these peptides to be drug-like molecules have been explored, and these include using biocompatible nano-carriers. ADEP1 analogues (SC005-8) conjugated to gelatin-capped Silver/Indium/Sulfide (AgInS 2 ) quantum dots (QDs) improved the antibacterial activity against Gram-negative ( Escherichia coli and Pseudomonas aeruginosa ), and Gram-positive ( Bacillus subtilis , Staphylococcus aureus and Methicillin-resistant Staphylococcus aureus ) bacteria. The ADEP1 analogues exhibited minimum inhibition concentrations (MIC) between 63 and 500 µM, and minimum bactericidal concentrations (MBC) values between 125 and 750 µM. The AgInS 2 -ADEP1 analogue conjugates showed enhanced antibacterial activity as evident from the MIC and MBC values, i.e., 1.6-25 µM and 6.3-100 µM, respectively. The AgInS 2 -ADEP1 analogue conjugates were non-toxic against HEK-293 cells at concentrations that showed antibacterial activity. The findings reported herein could be helpful in the development of antibacterial treatment strategies.

The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Here we review progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways. Finally, we briefly discuss issues involved in making Reactome more fully interoperable with other related resources such as the Gene Ontology and maintaining the resulting community resource network., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)