bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of Socioeconomic Factors on Time to Surgery for Distal Radius Fractures
Authors: Marxen Troy , Stewart Chris , Razavi Amir , Payne Sam , Ghareeb Paul
Published: May 2024

Background:

Delay in care secondary to socioeconomic status (SES) and demographic factors represents an area for potential improvement. Reducing time to surgery in distal radius fracture (DRF) fixation may improve outcomes while reducing cost. The purpose of this study is to investigate the effect of SES on time to surgery in our study population.

Methods:

Patients undergoing outpatient DRF surgery within an academic healthcare system during a 4-year period were reviewed. Time to surgery and demographic factors were analyzed. The US Census Bureau was used to determine median household income (MHI) for a patient’s ZIP code; patients were stratified into three groups based on MHI.

Results:

A total of 413 patients met inclusion criteria. SES (14.7 d in the low-SES group, 14.0 d in the mid-SES group, and 11.1 d in the high-SES group, P = 0.00063), insurance (11.7 d for insured versus 16.3 d for Medicaid/uninsured, P < 0.0001), race (non-White group: 15.2 d versus White group: 10.9 d, P < 0.0001), and treatment facility (16.2 d at county hospital versus 10.9 d at university hospital, P < 0.0001) were associated with time to surgery in univariate analysis. Multivariate analysis found that only treatment facility was associated with time to surgery.

Conclusions:

Non-White, uninsured/Medicaid individuals residing in low-SES areas may be more likely to receive care at a safety-net facility and are at greatest risk for delay in time to surgery. Measures aimed to reduce barriers to care, increase healthcare coverage, and improve patient education should be initiated to mitigate these disparities.
Implementation of anterior segment ophthalmic telemedicine
Authors: Armstrong Grayson W. , Liebman Daniel L. , Ashourizadeh Helia
Published: May 2024

Purpose of review

The growing push to integrate telemedicine into ophthalmic practices requires physicians to have a thorough understanding of ophthalmic telemedicine's applications, limitations, and recent advances in order to provide well tolerated and appropriate clinical care. This review aims to provide an overview of recent advancements in the use of ophthalmic telemedicine for anterior segment eye examinations.

Recent findings

Virtual care for anterior segment evaluation relies on appropriate technology, novel workflows, and appropriate clinical case selection. Recent advances, particularly in the wake of the COVID-19 pandemic, have highlighted the utility of home-based assessments for visual acuity, external evaluation, tonometry, and refraction. Additionally, innovative workflows incorporating office-based testing into virtual care, termed ‘hybrid telemedicine’, enable high-quality ophthalmic testing to inform clinical decision-making.

Novel digital tools and workflows enable high-quality anterior segment evaluation and management for select ophthalmic concerns. This review highlights the clinical tools and workflows necessary to enable anterior segment telehealth.
Effectiveness of a Patient Safety Incident Disclosure Education Program: A Quasi-Experimental Study
Authors: KIM Mi Young , KIM Yujeong
Published: May 2024

Background

The accurate disclosure of patient safety incidents is necessary to minimize patient safety incidents and medical disputes. As prospective healthcare providers, nursing students need to possess the ability to disclose patient safety incidents.

Purpose

This study was designed to investigate the effect of a patient safety incident disclosure education program for undergraduate nursing students on participants' knowledge and perception of disclosure of these incidents, attitudes toward patient safety, and self-efficacy regarding disclosure of these incidents.

Methods

A quasi-experimental study with a nonequivalent pretest–posttest design was conducted on fourth-year undergraduate nursing students recruited between September 6 and October 22, 2021, through convenience sampling from two universities in South Korea. The experimental group (n = 25) received the education program. The control group (n = 25) received educational materials on the disclosure of patient safety incidents only. Knowledge and perceptions of patient safety incident disclosure, attitudes toward patient safety, and self-efficacy regarding incident disclosure were measured. Data were analyzed using descriptive analysis, t test, χ2 test, Fisher's exact test, Mann–Whitney U test, Wilcoxon signed-rank test, and ranked analysis of covariance.

Results

Posttest results revealed knowledge (p < .001), perceptions (p = .031), and self-efficacy (p < .001) with regard to the disclosure of patient safety incidents were all significantly higher in the experimental group than in the control group. Posttest attitudes toward patient safety were not significantly different between the two groups (p = .908).

Conclusions/Implications for Practice

The patient safety incident disclosure education program effectively enhances the knowledge, perception, and self-efficacy of nursing students with regard to safety incidents. The findings may be used to improve training and educational programs in nursing colleges and hospitals to improve the knowledge, perception, and self-efficacy of nursing students with regard to disclosing patient safety incidents in clinical settings.
Development of a Novel Evidence-Based Practice-Specific Competency for Doctor of Physical Therapy Students in Clinical Education: A Modified Delphi Approach
Authors: Haladay Douglas , Morris Zoe , Tilson Julie , Fitzgerald Caitlin , Applebaum Donna , Flom-Meland Cindy , DeWaay Deborah , Manal Tara Jo , Gravano Tamara , Anderson Stephanie , Miro Rebecca , Russ David , Klein Aimee
Published: May 2024

Introduction.

Evidence-based practice (EBP) results in high-quality care and decreases unwarranted variation in practice.

Review of the Literature.

Few performance criteria related to EBP are included in physical therapy clinical education (CE) performance measures, despite EBP requirements in Doctor of Physical Therapy education. The purpose of this study was to develop EBP-specific competencies that may be used for Doctor of Physical Therapy students for use throughout CE.

Subjects.

Thirteen subject matter experts (SME) participated in this study.

Methods.

Subject matter experts were asked to rank each core EBP competency, from a previously described framework, using a 3-point Likert scale, which included “Not Essential,” “Essential,” and “Not Sure.” A consensus of 70% or greater for the “Essential” rating advanced the competency to the final Delphi round, whereas a consensus of 70% or greater for the “Not Essential” rating was required for competency elimination. Subject matter experts voted to either “Accept” or “Modify” the competencies that had reached the inclusion consensus threshold. All competencies that reached consensus for inclusion after all 3 rounds were included in the final EBP Domain of Competence.

Results.

Consensus was achieved in round one for 38% (n = 26) of items. In round 2, a consensus was achieved for 20% (n = 8) of items. Of the items remaining after rounds 1 and 2, 6 overarching competencies were identified, and all remaining items served as descriptions and specifications in the final EBP Domain of Competence.

Discussion and Conclusions.

The 6 competencies developed from this study constitute the EBP Domain of Competence and may be used throughout CE to assess students' EBP competency in clinical practice.
Protease activated receptor-4: ready to be part of the antithrombosis spectrum
Authors: Andrianova Izabella , Kowalczyk Mia , Denorme Frederik
Published: May 2024

Purpose of review

Cardiovascular disease is a major cause of death worldwide. Platelets play a key role in this pathological process. The serine protease thrombin is a critical regulator of platelet reactivity through protease activated receptors-1 (PAR1) and PAR4. Since targeting PAR4 comes with a low chance for bleeding, strategies blocking PAR4 function have great antithrombotic potential. Here, we reviewed the literature on platelet PAR4 with a particular focus on its role in thromboinflammation.

Recent findings

Functional PAR4 variants are associated with reduced venous thrombosis risk (rs2227376) and increased risk for ischemic stroke (rs773902). Recent advances have allowed for the creation of humanized mouse lines in which human PAR4 is express instead of murine PAR4. This has led to a better understanding of the discrepancies between human and murine PAR4. It also made it possible to introduce single nucleotide polymorphisms (SNPs) in mice allowing to directly test the in vivo functional effects of a specific SNP and to develop in vivo models to study mechanistic and pharmacologic alterations induced by a SNP.

PAR4 plays an important role in cardiovascular diseases including stroke, myocardial infarction and atherosclerosis. Targeting PAR4 hold great potential as a safe antithrombotic strategy.
Patient Surveillance Adherence After Treatment for Endometrial Cancer
Authors: Zhang Naixin , Marshall Lila , Thappa Sarah , Morell Alexandra , Samborski Alexandra , Moore Richard , Wilbur MaryAnn
Published: May 2024

BACKGROUND:

To assess factors that may affect patients' adherence to recommended surveillance after treatment for endometrial cancer.

METHODS:

We performed a retrospective study of all patients undergoing primary treatment for endometrial cancer from January 1, 2010, to December 30, 2017, at a tertiary referral center. Patients were included for analysis if there was sufficient information in the electronic medical records. Patient demographic information, cancer characteristics, and surveillance adherence data were collected. The median inflation-adjusted income was calculated from the patients' ZIP codes and U.S. Census data. The primary outcome assessed was adherence to surveillance, defined as two or more visits per 12 months in individuals at low risk and four or more visits per 12 months in individuals at high risk, consistent with recommended guidelines.

RESULTS:

During the study period, 870 patients were included for analysis. The mean age at diagnosis and body mass index (BMI) of the entire cohort were 63.4 years and 35.8, respectively. Overall, 761 patients (87.5%) were adherent to the recommended surveillance guidelines. Patients who were not adherent to recommended surveillance lived significantly farther from the cancer center (39.2 miles vs 20.7 miles, P=.026) and had a significantly lower median inflation-adjusted income ($74,015 vs $80,435, P=.027).

CONCLUSION:

Increased distance to a tertiary care center and lower median income were significantly associated with decreased adherence to recommended surveillance guidelines. This is consistent with current literature on increased distance traveled as a proxy for worse survival in gynecologic malignancies, as well as worse endometrial cancer outcomes in patients of lower socioeconomic status. This highlights an area of disparity that needs improvement and warrants further investigation.
Low cabotegravir trough concentrations without oral lead-in in patients with HIV-1 switching to long-acting cabotegravir and rilpivirine
Authors: Rubenstein Emma , Diemer Myriam , Goldwirt Lauriane , Lascoux-Combe Caroline , Chaix Marie-Laure , Rami Agathe , Ponscarme Diane , Lafaurie Matthieu , Denis Blandine , De Castro Nathalie , Gras Julien , Liegeon Geoffroy , Sellier Pierre-Olivier , Deville Laure , Chevret Sylvie , Delaugerre Constance , Molina Jean-Michel
Published: May 2024

In a cohort of 72 consecutive virologically-suppressed patients with HIV-1 switching to long-acting cabotegravir and rilpivirine, we observed low cabotegravir trough concentrations 1 and 3 months after the first injection, with a significant association with no oral lead-in at 1 month [odds ratio (OR) = 6.3 [95% confidence interval (CI) 1.7–29.5], P = 0.01] and three months (OR = 5.6 [95% CI 1.3–29.7], P = 0.03), and with high BMI at 1 month (OR = 1.3 [95% CI 1.1–1.6], P = 0.007).
EFFICACY OF A SEPSIS CLINICAL DECISION SUPPORT SYSTEM IN IDENTIFYING PATIENTS WITH SEPSIS IN THE EMERGENCY DEPARTMENT
Authors: Hou Yueh-Tseng , Wu Meng-Yu , Chen Yu-Long , Liu Tzu-Hung , Cheng Ruei-Ting , Hsu Pei-Lan , Chao An-Kuo , Huang Ching-Chieh , Cheng Fei-Wen , Lai Po-Lin , Wu I-Feng , Yiang Giou-Teng
Published: May 2024

Background: Early prediction of sepsis onset is crucial for reducing mortality and the overall cost burden of sepsis treatment. Currently, few effective and accurate prediction tools are available for sepsis. Hence, in this study, we developed an effective sepsis clinical decision support system (S-CDSS) to assist emergency physicians to predict sepsis. Methods: This study included patients who had visited the emergency department (ED) of Taipei Tzu Chi Hospital, Taiwan, between January 1, 2020, and June 31, 2022. The patients were divided into a derivation cohort (n = 70,758) and a validation cohort (n = 27,545). The derivation cohort was subjected to 6-fold stratified cross-validation, reserving 20% of the data (n = 11,793) for model testing. The primary study outcome was a sepsis prediction (International Classification of Diseases, Tenth Revision, Clinical Modification) before discharge from the ED. The S-CDSS incorporated the LightGBM algorithm to ensure timely and accurate prediction of sepsis. The validation cohort was subjected to multivariate logistic regression to identify the associations of S-CDSS-based high- and medium-risk alerts with clinical outcomes in the overall patient cohort. For each clinical outcome in high- and medium-risk patients, we calculated the sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios, and accuracy of S-CDSS-based predictions. Results: The S-CDSS was integrated into our hospital information system. The system featured three risk warning labels (red, yellow, and white, indicating high, medium, and low risks, respectively) to alert emergency physicians. The sensitivity and specificity of the S-CDSS in the derivation cohort were 86.9% and 92.5%, respectively. In the validation cohort, high- and medium-risk alerts were significantly associated with all clinical outcomes, exhibiting high prediction specificity for intubation, general ward admission, intensive care unit admission, ED mortality, and in-hospital mortality (93.29%, 97.32%, 94.03%, 93.04%, and 93.97%, respectively). Conclusion: Our findings suggest that the S-CDSS can effectively identify patients with suspected sepsis in the ED. Furthermore, S-CDSS-based predictions appear to be strongly associated with clinical outcomes in patients with sepsis.
SP1 MEDIATES OGD/R-INDUCED CARDIOMYOCYTE INJURY VIA ENHANCING THE TRANSCRIPTION OF USP46
Authors: Ma Xuming , Wang Luzhen , Li Wanpeng , Huang Yan , Zhu Yan , Li Jing
Published: May 2024

Background: One of the mechanisms responsible for the high mortality rate of acute myocardial infarction is myocardial ischemia-reperfusion injury (MI-RI). The present study focused on the role and regulatory mechanisms of specificity protein 1 (SP1) and ubiquitin-specific protease 46 (USP46) in oxygen-glucose deprivation/reperfusion (OGD/R)-induced cardiomyocyte injury. Methods: OGD/R was used to treat cardiomyocytes AC16 to mimic ischemia-reperfusion in vitro. Cell viability, proliferation, and apoptosis were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, 5-ethynyl-2′-deoxyuridine, and flow cytometry assays. Enzyme-linked immunosorbent assays analyzed the concentrations of TNF-α and IL-1β. Several protein levels were analyzed by western blotting. The levels of iron (Fe2+), reactive oxygen species, malondialdehyde, and the activities of superoxide dismutase were analyzed by commercial kits. Chromatin immunoprecipitation and dual-luciferase report assays assessed the relationship between USP46 and SP1. Results: USP46 and SP1 were upregulated in serum from MI patients and they had a positive correlation. OGD/R stimulation suppressed cardiomyocyte viability and proliferation, as well as induced cardiomyocyte inflammation, oxidative stress (OxS) injury, apoptosis, and ferroptosis, but these effects were impaired by USP46 or SP1 knockdown. SP1 could enhance the transcription of USP46, and USP46 overexpression reversed SP1 silencing-mediated effects on OGD/R-induced cardiomyocytes. SP1 mediated the AMPK signaling via USP46. Conclusion: SP1 mediated OGD/R-induced cardiomyocyte inflammation, OxS injury, apoptosis, and ferroptosis by inactivating the AMPK signaling via enhancing the transcription of USP46.
Mechanistic insights into behavioral clusters associated with cancer-related systemic inflammatory response
Authors: Goto Taichi , Saligan Leorey N.
Published: May 2024

Purpose of review

This focused, narrative review mostly describes our team’s investigations into the potential inflammatory mechanisms that contribute to the development of cancer-related gastrointestinal (GI) mucositis and its associated symptoms. This review summarizes details of our clinical and preclinical findings to test the role of inflammation in the development and occurrence of these cancer-related conditions.

Recent findings

GI mucositis (GIM) is a common, distressing condition reported by cancer patients. GIM is often clustered with other behaviors including fatigue, pain, anorexia, depression, and diarrhea. It is hypothesized that there is a common biologic mechanism underpinning this symptom cluster. Our multi-platform investigations revealed that GIM and its associated cluster of behaviors may be triggered by local inflammation spreading systemically causing pro-inflammatory-mediated toxicities, leading to alterations in immune, metabolic, and nervous system functions and activities. For example, behavioral toxicities related to local irradiation for non-metastatic cancer may be triggered by mGluR5 activation influencing prolonged T cell as well as NF-κB transcription factor activities. Thus, interventions targeting inflammation and associated pathways may be a reasonable strategy to alleviate GIM and its symptom cluster.

GIM may be a sign of a broader systemic inflammatory response triggered by cancer or its treatment. Addressing GIM and its associated symptoms primarily involves supportive care strategies focused on relieving symptoms, promoting healing, and preventing complications.
Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation
Authors: Hera Mahmudur Rahman , Koslicki David
Published: May 2024

Motivation

The increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizingk-mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash has emerged as a popular sketching technique and has been used in several useful applications. Recent studies on FracMinHash proved unbiased estimators for the containment and Jaccard indices. However, theoretical investigations for other metrics, such as the cosine similarity, are still lacking.

Theoretical contributions

In this paper, we present a theoretical framework for estimating cosine similarity from FracMinHash sketches. We establish conditions under which this estimation is sound, and recommend a minimum scale factorsfor accurate results. Experimental evidence supports our theoretical findings.

Practical contributions

We also presentfrac-kmc, a fast and efficient FracMinHash sketch generator program.frac-kmcis the fastest known FracMinHash sketch generator, delivering accurate and precise results for cosine similarity estimation on real data. We show that by computing FracMinHash sketches usingfrac-kmc, we can estimate pairwise cosine similarity speedily and accurately on real data.frac-kmcis freely available here:https://github.com/KoslickiLab/frac-kmc/.

2012

ACM Subject Classification

Applied computing → Computational biology
Semi-Supervised Learning to Boost Cardiotoxicity Prediction by Mining a Large Unlabeled Small Molecule Dataset
Authors: Arab Issar , Laukens Kris , Bittremieux Wout
Published: May 2024

Predicting drug toxicity is a critical aspect of ensuring patient safety during the drug design process. Although conventional machine learning techniques have shown some success in this field, the scarcity of annotated toxicity data poses a significant challenge in enhancing models’ performance. In this study, we explore the potential of leveraging large unlabeled datasets using semi-supervised learning to improve predictive performance for cardiotoxicity across three targets: the voltage-gated potassium channel (hERG), the voltage-gated calcium channel (Cav1.2), and the voltage-gated sodium channel (Nav1.5). We extensively mined the ChEMBL database, comprising approximately 2 million small molecules, then employed semi-supervised learning to construct robust classification models for this purpose. We achieved a performance boost on highly diverse (i.e. structurally dissimilar) test datasets across all three targets. Using our built models, we screened the whole ChEMBL database and a large set of FDA-approved drugs, identifying several compounds with potential cardiac channel activity. To ensure broad accessibility and usability for both technical and non-technical users, we developed a cross-platform graphical user interface that allows users to make predictions and gain insights into the cardiotoxicity of drugs and other small molecules. The software is made available as open source under the permissive MIT license athttps://github.com/issararab/CToxPred2.
Cliffy: robust 16S rRNA classification based on a compressed LCA index
Authors: Ahmed Omar , Boucher Christina , Langmead Ben
Published: May 2024

Taxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with ther-index enable full-text pattern matching against large sequence collections. But the data structures that link pattern sequences to their clades of origin still do not scale well to large collections. Previous work proposed the document array profiles, which use𝒪(rd) words of space whereris the number of maximal-equal letter runs in the Burrows-Wheeler transform anddis the number of distinct genomes. The linear dependence ondis limiting, since real taxonomies can easily contain 10,000s of leaves or more. We propose a method called cliff compression that reduces this size by a large factor, over 250x when indexing the SILVA 16S rRNA gene database. This method uses Θ(rlogd) words of space in expectation under a random model we propose here. We implemented these ideas in an open source tool called Cliffy that performs efficient taxonomic classification of sequencing reads with respect to a compressed taxonomic index. When applied to simulated 16S rRNA reads, Cliffy’s read-level accuracy is higher than Kraken2’s by 11-18%. Clade abundances are also more accurately predicted by Cliffy compared to Kraken2 and Bracken. Overall, Cliffy is a fast and space-economical extension to compressed full-text indexes, enabling them to perform fast and accurate taxonomic classification queries.

2012 ACM Subject Classification

Applied computing→Computational genomics
Distinct mechanisms of non-autonomous UPRERmediated by GABAergic, glutamatergic, and octopaminergic neurons
Authors: Coakley Aeowynn J. , Hruby Adam J. , Wang Jing , Bong Andrew , Nair Tripti , Ramos Carmen M. , Alcala Athena , Hicks Daniel , Averbukh Maxim , Dutta Naibedya , Moaddeli Darius , Siebrand Cynthia , de los Rios Rogers Mattias , Sahay Arushi , Curran Sean P. , Mullen Peter J. , Benayoun Bérénice A , Garcia Gilberto , Higuchi-Sanabria Ryo
Published: May 2024

The capacity to deal with stress declines during the aging process, and preservation of cellular stress responses is critical to healthy aging. The unfolded protein response of the endoplasmic reticulum (UPRER) is one such conserved mechanism, which is critical for the maintenance of several major functions of the ER during stress, including protein folding and lipid metabolism. Hyperactivation of the UPRERby overexpression of the major transcription factor,xbp-1s, solely in neurons drives lifespan extension as neurons send a neurotransmitter-based signal to other tissue to activate UPRERin a non-autonomous fashion. Previous work identified serotonergic, dopaminergic, and tyraminergic neurons in this signaling paradigm. To further expand our understanding of the neural circuitry that underlies the non-autonomous signaling of ER stress, we activated UPRERsolely in glutamatergic, octopaminergic, and GABAergic neurons inC. elegansand paired whole-body transcriptomic analysis with functional assays. We found that UPRER-induced signals from glutamatergic neurons increased expression of canonical protein homeostasis pathways and octopaminergic neurons promoted pathogen response pathways; while minor, statistically significant changes were observed in lipid metabolism-related genes with GABAergic UPRERactivation. These findings provide further evidence for the distinct role neuronal subtypes play in driving the diverse response to ER stress.
Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates
Authors: Gahan James M. , Helfrich Lily W. , Wetzel Laura A. , Bhanu Natarajan V. , Yuan Zuo-Fei , Garcia Benjamin A. , Klose Rob , Booth David S.
Published: May 2024

Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding of how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate this possibility, here we examine chromatin-based gene regulatory features in the closest relatives of animals, choanoflagellates. UsingSalpingoeca rosettaas a model system, we examined chromatin accessibility and histone modifications at the genome scale and compared these features to gene expression. We first observed that accessible regions of chromatin are primarily associated with gene promoters and found no evidence of distal gene regulatory elements resembling the enhancers that animals deploy to regulate developmental gene expression. Remarkably, a histone modification deposited by polycomb repressive complex 2, histone H3 lysine 27 trimethylation (H3K27me3), appeared to function similarly inS. rosettato its role in animals, because this modification decorated genes with cell type-specific expression. Additionally, H3K27me3 marked transposons, retaining what appears to be an ancestral role in regulating these elements. We further uncovered a putative new bivalent chromatin state at cell type-specific genes that consists of H3K27me3 and histone H3 lysine 4 mono-methylation (H3K4me1). Together, our discoveries support the scenario that gene-associated histone modification states that underpin development emerged before the evolution of animal multicellularity.
Photoactivatable Plasma Membrane Probe Through Self-Triggered Photooxidation Cascade for Live Super-Resolution Microscopy
Authors: Pfister Sonia , Le Berruyer Valentine , Fam Kyong , Collot Mayeul
Published: May 2024

Super-resolution imaging based on the localization of single emitters requires a spatio-temporal control of the ON and OFF state. To this end, photoactivatable fluorophores are adapted as they can be turned on upon light irradiation. Here we present a concept called Self-Triggered Photooxidation Cascade (STPC) based on the photooxidation of a plasma membrane targeted leuco-rhodamine (LRhod-PM), a non-fluorescent reduced form of a rhodamine probe. Upon visible light irradiation the small number of oxidized rhodamines, Rhod-PM, acts as a photosensitizer to generate singlet oxygen capable to oxidize the OFF state LRhod-PM. We showed that this phenomenon is kinetically favored by a high local concentration and propagates quickly when the probe is embedded in membrane bilayers. In addition, we showed that the close proximity of the dyes favors the photobleaching. At the single-molecule level, the concomitant activation/bleaching phenomena allow reaching a single-molecule blinking regime enabling single-molecule localization microscopy for super-resolution of live cellular membranes.
LiF-MS+, a revised technique for mapping peptide-protein interactions
Authors: Parker Benjamin , Weiss Eric
Published: May 2024

Short linear motifs are sequences of amino acids present in unstructured polypeptide regions that function as ligands for specific sites on folded protein domains. These interactions, which often occur with low to modest affinity, modulate dynamic biological processes such as signal transduction and membrane trafficking. We recently described Ligand Footprinting-Mass Spectrometry (LiF-MS), a technique that rapidly and precisely maps sites at which short peptide ligands bind their biologically relevant recognition sites on folded protein domains. This approach marks the binding location of a peptide ligand on a structured protein using a cleavable crosslinker appended to the ligand that leaves behind a stable chemical modification following cleavage. This modification serves as a mass tag detectable by mass spectrometry, pinpointing sites of peptide ligand binding. Here we present LiF-MS+, an improved version of the footprinting technique that replaces the butanol mass tag with 1-butylpyrrolidine, which is positively charged at neutral pH and thus aids in ionization of the crosslinked peptide for analysis by mass spectrometry. We show ligand-mediated butylpyrrolidine footprinting effectively maps the well characterized binding interaction of the p38α mitogen-activated protein kinase (MAPK) with a MKK6 D-motif short linear motif peptide ligand, uncovering additional binding site information not observed in our original experiment. LiF-MS+ is thus a straightforward improvement of our previously published methodology for mapping the binding of short linear motifs to folded protein domains.
LiveLattice: Real-time visualization of tilted light-sheet microscopy data using a memory-efficient transformation algorithm
Authors: Wang Zichen , Hakozaki Hiroyuki , McMahon Gillian , Medina-Carbonero Marta , Schöneberg Johannes
Published: May 2024

Light-sheet fluorescence microscopy (LSFM), a prominent fluorescence microscopy technique, offers enhanced temporal resolution for imaging biological samples in four dimensions (4D; x, y, z, time). Some of the most recent implementations, including inverted selective plane illumination microscopy (iSPIM) and lattice light-sheet microscopy (LLSM), rely on a tilting of the sample plane with respect to the light sheet of 30-45 degrees to ease sample preparation. Data from such tilted-sample-plane LSFMs require subsequent deskewing and rotation for proper visualization and analysis. Such transformations currently demand substantial memory allocation. This poses computational challenges, especially with large datasets. The consequence is long processing times compared to data acquisition times, which currently limits the ability for live-viewing the data as it is being captured by the microscope. To enable the fast preprocessing of large light-sheet microscopy datasets without significant hardware demand, we have developed WH-Transform, a novel GPU-accelerated memory-efficient algorithm that integrates deskewing and rotation into a single transformation, significantly reducing memory requirements and reducing the preprocessing run time by at least 10-fold for large image stacks. Benchmarked against conventional methods and existing software, our approach demonstrates linear scalability. Processing large 3D stacks of up to 15 GB is now possible within one minute using a single GPU with 24 GB of memory. Applied to 4D LLSM datasets of human hepatocytes, human lung organoid tissue, and human brain organoid tissue, our method outperforms alternatives, providing rapid, accurate preprocessing within seconds. Importantly, such processing speeds now allow visualization of the raw microscope data stream in real time, significantly improving the usability of LLSM in biology. In summary, this advancement holds transformative potential for light-sheet microscopy, enabling real-time, on-the-fly data processing, visualization, and analysis on standard workstations, thereby revolutionizing biological imaging applications for LLSM, SPIM and similar light microscopes.
GWAS reveals Genetic Susceptibility to Air Pollution-Related Asthma Exacerbations in Children of African Ancestry
Authors: Kelchtermans Jelte , March Michael E. , Mentch Frank , Liu Yichuan , Nguyen Kenny , Hakonarson Hakon
Published: May 2024

Background

The relationship between ambient air pollution (AAP) exposure and asthma exacerbations is well-established. However, mitigation efforts have yielded mixed results, potentially due to genetic variability in the response to AAP. We hypothesize that common single nucleotide polymorphisms (SNPs) are linked to AAP sensitivity and test this through a Genome Wide Association Study (GWAS).

Methods

We selected a cohort of pediatric asthma patients frequently exposed to AAP. Patients experiencing exacerbations immediately following AAP spikes were deemed sensitive. A GWAS compared sensitive versus non-sensitive patients. Findings were validated using data from the All of Us program.

Results

Our study included 6,023 pediatric asthma patients. Due to the association between AAP exposure and race, GWAS analysis was feasible only in the African ancestry cohort. Seven risk loci reached genome-wide significance, including four non-intergenic variants. Two variants were validated: rs111970601 associated with sensitivity to CO (odds ratio [OR], 6.58; PL=L1.63L×L10−8; 95% CI, 3.42-12.66) and rs9836522 to PM2.5 sensitivity (OR 0.75; PL=L3,87 ×L10−9; 95% CI, 0.62-0.91).

Interpretation

While genetic variants have been previously linked to asthma incidence and AAP exposure, this study is the first to link specific SNPs with AAP-related asthma exacerbations. The identified variants implicate genes with a known role in asthma and established links to AAP. Future research should explore how clinical interventions interact with genetic risk to mitigate the effects of AAP, particularly to enhance health equity for vulnerable populations.

What is already known on this topic

The relationship between ambient air pollution (AAP) exposure and asthma exacerbations is well-established. However, efforts to mitigate the impact of AAP on children with asthma have yielded mixed results, potentially due to genetic variability in response to AAP.

What this study adds

Using publicly available AAP data, we identify which children with asthma experience exacerbations immediately following spikes in AAP. We then conduct a Genome Wide Association Study (GWAS) comparing these patients with those who have no temporal association between AAP spikes and asthma exacerbations, identifying several Single Nucleotide Polymorphisms (SNPs) significantly associated with AAP sensitivity.

How this study might affect research, practice, or policy

While genetic variants have previously been linked to asthma incidence and AAP exposure, this study is the first to link specific SNPs with AAP-related asthma exacerbations. This creates a framework for identifying children especially at risk when exposed to AAP. These children should be targeted with policy interventions to reduce exposure and may require specific treatments to mitigate the effects of ongoing AAP exposure in the interim.
More Than Words: An Integrative Review of Innovative Elicitation Techniques for Qualitative Interviews
Authors: Kahlke Renate , Maggio Lauren A. , Lee Mark , Cristancho Sayra , LaDonna Kori , Abdallah Zahra , Khehra Aakashdeep , Kshatri Kushal , Horsley Tanya , Varpio Lara
Published: May 2024

Introduction

Interviews are central to many qualitative studies in health professions education (HPE). However, researchers often rely only on oral questioning despite the existence of techniques tailored to elicit the rich data needed to address complex problems and meaningfully engage participants. Elicitation techniques are strategies – e.g. participant photography, neighbourhood walks – used to generate rich conversations, but guidance on these techniques is scattered across literatures from diverse fields. In this synthesis, we offer an overview of the elicitation techniques available and advice about how to choose between them.

Methods

We conducted an integrative review, drawing on methodological literature from across the health and social sciences. Our interdisciplinary searches yielded 3056 citations. We included 293 citations that were methodologically focused and discussed elicitation techniques used in interviews with adults. We then extracted specific elicitation techniques, summarizing each technique to capture key features, as well as strengths and weaknesses. From this, we developed a framework to help researchers identify challenges in their interview-based research, and to select elicitation techniques that address their challenges.

Results

Elicitation techniques serve two main purposes: they can enrich data and engage participants in new ways. To enrich data, researchers might seek to shift conversations away from participants’ entrenched narratives, to externalize conversations on sensitive topics, or to elicit affect, tacit knowledge, or contextual details. When engaging participants in new ways, researchers might seek to increase equity between the researcher and participant or interview accessibility across diverse participant populations.

Discussion

When chosen with study goals in mind, elicitation techniques can enrich interview data. To harness this potential, we need to re-conceptualize interviews as co-production of knowledge by researcher(s) and participant(s). To make interviews more accessible, we need to consider flexibility so that each participant can engage in ways that best suit their needs and preferences.
A core outcome set for adult general ICU patients
Authors: Kjær Maj-Brit Nørregaard , Bruun Camilla Rahbek Lysholm , Granholm Anders , Møller Morten Hylander , Rasmussen Bodil Steen , Mortensen Camilla Bekker , Poulsen Lone Musaeus , Strøm Thomas , Laerkner Eva , Brøchner Anne Craveiro , Haberlandt Trine , Bunzel Anne-Marie Gellert , Herløv Louise Stenbryggen , Holm Anna , Sivapalan Praleene , Estrup Stine , Cronhjort Maria , Schandl Anna , Laake Jon Henrik , Hofsø Kristin , Blokzijl Fredrike , Keus Frederic , Pfortmueller Carmen Andrea , Ostermann Marlies , Cole Jade M , Wise Matt P , Szczeklik Wojciech , Wludarczyk Anna , Jovaiša Tomas , Cecconi Maurizio , Sigurdsson Martin Ingi , Nalos Marek , Hästbacka Johanna , Mäkinen Marja , Hammond Naomi , Litton Edward , Haines Kimberley , Myatra Sheila Nainan , Tirupakuzhi Vijayaraghavan Bharath Kumar , Yadav Kavita , Jha Vivekanand , Venkatesh Balasubramanian , Egerod Ingrid , Perner Anders , Collet Marie O
Published: May 2024

Purpose

Randomised clinical trials should ideally use harmonised outcomes that are important to patients and to facilitate meta-analyses and ensuring generalisability. Core outcome sets for specific subsets of ICU patients exist, e.g., respiratory failure, delirium, and COVID-19, but not for ICU patients in general. Accordingly, we aimed to develop a core outcome set for adult general ICU patients.

Methods

We developed a core outcome set in Denmark following the Core Outcome Measures in Effectiveness Trials (COMET) Handbook. We used a modified Delphi consensus process with multiple methods design, including literature review, survey, semi-structured interviews, and discussions with initially five Danish research panels, involving adult ICU survivors, family members, clinicians, and researchers. The core outcome set was internationally validated in local panels in 14 countries and revised accordingly.

Results

We identified 329 published outcomes, of which 50 were included in the 264 participant Delphi survey. After 82 semi-structured survey participant interviews no additional outcomes were added. The first survey round was completed by 249 (94%) participants, and 202 (82%) contributed to the final third round. The initial core outcome set comprised six core outcomes. International validation involved 217 research panel members and resulted in the final core outcome set of survival, free of life support, free of delirium, out of hospital, health-related quality of life, and cognitive function.

Conclusions

We developed and internationally validated a core outcome set with six core outcomes to be used in research, specifically clinical trials involving adult general ICU patients.
Formate from THF-C1 metabolism induces the AOX1 promoter in formate dehydrogenase-deficientPichia pastoris
Authors: Bustos Cristina , Berrios Julio , Fickers Patrick
Published: May 2024

InPichia pastoris(Komagataella phaffii), formate is a recognized alternative inducer to methanol for expression systems based on the AOX1 promoter (pAOX1). By disrupting the formate dehydrogenase encodingFDH1gene, we converted such a system into a self-induced one, as adding any inducer in the culture medium is no longer requested for pAOX1 induction. In cells, formate is generated from serine through the THF-C1 metabolism, and it cannot be converted into carbon dioxide in anfdh1Δ strain. Under non-repressive culture conditions, such as on sorbitol, the intracellular formate generated from the THF-C1 metabolism is sufficient to induce pAOX1 and initiate protein synthesis. This was evidenced for two model proteins, namely intracellular eGFP and secreted CalB lipase fromC. antarctica. Similar protein productivities were obtained for anfdh1Δ strain on sorbitol and a non-disrupted strain on sorbitol-methanol. Considering aP. pastoris fdh1Δstrain as a workhorse for recombinant protein synthesis paves the way for the further development of methanol-free processes inP. pastoris.
Evaluating apoptotic gene efficiency for CHO culture performance using targeted integration
Authors: Catalán-Tatjer David , Ganesan Saravana Kumar , Martínez-Monge Iván , Grav Lise M. , Lavado-García Jesús , Nielsen Lars K.
Published: May 2024

Chinese hamster ovary (CHO) cells have long been the favoured platform for producing complex biopharmaceuticals such as monoclonal antibodies (mAbs). Cell death is a critical factor in all CHO cultures, dictating duration until harvest in batch cultures and viable cell density in perfusion. The programmed cell death, or apoptosis, pathway has been widely studied due to its relevance in affecting cell culture performance and the extensive knowledge about its protein-to-protein interaction network. However, clonal variation seen with random integration has confounded results and it remains unclear which effector genes should be overexpressed. Here, we employed the recombinase-mediated cassette exchange (RMCE) strategy to develop isogenic cell lines expressing one copy of erythropoietin, as model protein product, and various anti-apoptotic genes: bcl-2 from CHO and human origin, bcl-xL from CHO and human origin, mcl-1 and bhrf-1. We tested the generated isogenic cell lines in the presence of sodium butyrate, a well-known apoptotic initiator, in batch culture. The most promising candidates were cultured in fed-batch in the microbioreactor ambr®15 system. The observed phenotype varied significantly depending on the overexpressed gene, therefore the metabolic differences were further characterized using multiplexed quantitative proteomics. We showed that overexpressing bcl-2 from CHO origin significantly improved productivity and established a methodology to successfully test candidate genes via targeted integration. This will enable future metabolic engineering strategies to be more comparable and overcome the challenges faced thus far.
Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis
Authors: Brunner Andreas , Morero Natalia Rosalia , Zhang Wanlu , Hossain M. Julius , Lampe Marko , Pflaumer Hannah , Halavatyi Aliaksandr , Peters Jan-Michael , Beckwith Kai S. , Ellenberg Jan
Published: May 2024

How cells establish the interphase genome organization after mitosis is incompletely understood. Using quantitative and super-resolution microscopy, we show that the transition from a Condensin to a Cohesin-based genome organization occurs dynamically over two hours. While a significant fraction of Condensins remains chromatin-bound until early Gl, Cohesin-STAGl and its boundary factor CTCF are rapidly imported into daughter nuclei in telophase, immediately bind chromosomes as individual complexes and are sufficient to build the first interphase TAD structures. By contrast, the more abundant Cohesin-STAG2 accumulates on chromosomes only gradually later in Gl, is responsible for compaction inside TAD structures and forms paired complexes upon completed nuclear import. 0ur quantitative time-resolved mapping of mitotic and interphase loop extruders in single cells reveals that the nested loop architecture formed by sequential action of two Condensins in mitosis is seamlessly replaced by a less compact, but conceptually similar hierarchically nested loop architecture driven by sequential action of two Cohesins.
Critical role of Gα12 and Gα13 proteins in TGF-β-induced myofibroblast differentiation
Authors: Reed Eleanor B. , Sitikov Albert , Hamanaka Robert B. , Cetin-Atalay Rengül , Mutlu Gökhan M. , Mongin Alexander A. , Dulin Nickolai O.
Published: May 2024

Myofibroblast differentiation, characterized by accumulation of cytoskeletal and extracellular matrix proteins by fibroblasts, is a key process in wound healing and pathogenesis of tissue fibrosis. Transforming growth factor-β (TGF-β) is the most powerful known driver of myofibroblast differentiation. TGF-β signals through transmembrane receptor serine/threonine kinases that phosphorylate Smad transcription factors (Smad2/3) leading to activation of transcription of target genes. Heterotrimeric G proteins mediate a distinct signaling from seven-transmembrane G protein coupled receptors, not commonly linked to Smad activation. We asked if G protein signaling plays any role in TGF-β-induced myofibroblast differentiation, using primary cultured human lung fibroblasts. Activation of Gαs by cholera toxin blocked TGF-β-induced myofibroblast differentiation without affecting Smad2/3 phosphorylation. Inhibition of Gαi by pertussis toxin, or siRNA-mediated combined knockdown of Gαq and Gα11 had no significant effect on TGF-β-induced myofibroblast differentiation. A combined knockdown of Gα12 and Gα13 resulted in a drastic inhibition of TGF-β-stimulated expression of myofibroblast marker proteins (collagen-1, fibronectin, smooth-muscle α-actin), with siGα12 being significantly more potent than siGα13. Mechanistically, a combined knockdown of Gα12 and Gα13 resulted in a substantially reduced phosphorylation of Smad2 and Smad3 in response to TGF-β, which was accompanied by a significant decrease in the expression of TGFβ receptors (TGFBR1, TGFBR2) and of Smad3 under siGα12/13 conditions. In conclusion, our study uncovers a novel role of Gα12/13 proteins in the control of TGF-β signaling and myofibroblast differentiation.