bluuebunny/crossref_metadata_2025 huggingface dataset:
Visual Performance and Higher Order Aberrations Obtained With Omafilcon A Dual-Focus and Single-Vision Contact Lens Designs
Authors: Valencia-Nieto Laura , Novo-Diez Andrea , Mangas-Alonso María , Rojas-López Alba , López-de la Rosa Alberto , López-Miguel Alberto
Published: December 2023

Objective:

The purpose of this study was to assess the visual performance and monochromatic higher-order aberrations (HOAs) obtained while wearing a MiSight dual-focus (DF) contact lenses (CL) in comparison with a single-vision contact lens (SVCL).

Methods:

A randomized, double-masked, cross-over study was performed. Participants were fitted with a DFCL and a SVCL composed of the same material (omafilcon A) and parameters. Logarithm of the Minimum Angle of Resolution high-contrast (100%) and low-contrast (10%) visual acuity (VA) and contrast sensitivity (CS) for 3, 6, 12, and 18 cycles per degree were measured. Higher-order aberrations were also evaluated using a Hartmann–Shack aberrometer with the CLs on.

Results:

Twenty-four subjects (21 females and 3 males) with a mean age of 21.9±1.9 years (range: 18–27) were included. Low-contrast VA was significantly lower with the DFCL regarding the SVCL design (0.39±0.23 vs 0.25±0.18, P=0.002). However, there were no differences in high-contrast VA between both CLs (−0.03±0.10 vs −0.09±0.14, P=0.187). Contrast sensitivity was lower with the DFCL under all spatial frequencies (P≤0.048). Second-, third-, fourth-, and fifth-order aberrations were significantly (P<0.001) higher for the DFCL. There were also significant differences between DFCL and SVCL in defocus (0.87±0.28 vs 0.16±0.35, P<0.001), oblique trefoil (−0.16±0.27 vs −0.01±0.08, P=0.005), vertical coma (0.13±0.17 vs 0.00±0.08, P=0.002), and spherical aberration (0.09±0.11 vs −0.02±0.05, P=0.002).

Conclusion:

Visual performance for detecting low-contrast targets is reduced when wearing MiSight DFCL compared with a SVCL with the same material. The main reason might be the induction of second-order and HOAs by the DFCL design.
Effect of Anterior Chamber Air on Central Corneal Thickness in Human Donor Eyes
Authors: Huertas-Bello Marcela , Seery Christopher W. , Sem Karen , Fout Elizabeth , Triglia Concetta , Eghrari Allen O. , Koo Ellen H.
Published: December 2023

Purpose:

The purpose of this study was to describe the effects of intracameral air on corneal edema.

Methods:

A laboratory investigation was performed on human donor corneas. Baseline pachymetry measurements through anterior segment optical coherence tomography and endothelial cell density were obtained for all corneas. Each pair of corneas was separated and randomly assigned to undergo air injection or Optisol-GS into a BIONIKO artificial anterior chamber for 5 minutes at physiologic intraocular pressure confirmed by digital palpation. Photographs were obtained immediately on connection of the cornea to the artificial anterior chamber and on completion of the 5 minutes of treatment, with anterior chamber air being exchanged for Optisol-GS. Pretreatment and posttreatment photographs were obtained. Immediately after treatment, pachymetry was again obtained on all corneas. Pachymetry data underwent statistical analysis.

Results:

Corneal pachymetry improved from 690.5 ± 126.6 to 576.1 ± 87.2 μm, yielding a 114.4 ± 50.4 μm improvement of pachymetry in the group with air injected into the anterior chamber. This was a significant improvement of pachymetry when compared with the group with Optisol-GS injected into the anterior chamber, which showed an improvement from 662.3 ± 126.5 to 613.5 ± 108.0 μm, yielding an improvement of 48.8 ± 34.3 μm.

Conclusions:

Injection of air into the anterior chamber leads to a significant decrease in corneal pachymetry. We thereby propose that injecting air intracamerally is an effective intraoperative intervention when visualization is negatively affected by corneal edema.
Induction of cluster headache after opening of adenosine triphosphate-sensitive potassium channels: a randomized clinical trial
Authors: Al-Khazali Haidar M. , Deligianni Christina I. , Pellesi Lanfranco , Al-Karagholi Mohammad Al-Mahdi , Ashina Håkan , Chaudhry Basit Ali , Petersen Anja Sofie , Jensen Rigmor H. , Amin Faisal Mohammad , Ashina Messoud
Published: December 2023

Activation of adenosine triphosphate-sensitive potassium (KATP) channels has been implicated in triggering migraine attacks. However, whether the opening of these channels provoke cluster headache attacks remains undetermined. The hallmark of cluster headache is a distinct cyclical pattern of recurrent, severe headache episodes, succeeded by intervals of remission where no symptoms are present. In our study, we enrolled 41 participants: 10 with episodic cluster headaches during a bout, 15 in the attack-free remission period, and 17 diagnosed with chronic cluster headaches. Over 2 distinct experimental days, participants underwent a continuous 20-minute infusion of levcromakalim, a KATP channel opener, or a placebo (isotonic saline), followed by a 90-minute observational period. The primary outcome was comparing the incidence of cluster headache attacks within the postinfusion observation period between the levcromakalim and placebo groups. Six of 10 participants (60%) with episodic cluster headaches in bout experienced attacks after levcromakalim infusion, vs just 1 of 10 (10%) with placebo (P = 0.037). Among those in the remission phase, 1 of 15 participants (7%) reported attacks after levcromakalim, whereas none did postplacebo (P = 0.50). In addition, 5 of 17 participants (29%) with chronic cluster headache had attacks after levcromakalim, in contrast to none after placebo (P = 0.037). These findings demonstrate that KATP channel activation can induce cluster headache attacks in participants with episodic cluster headaches in bout and chronic cluster headache, but not in those in the remission period. Our results underscore the potential utility of KATP channel inhibitors as therapeutic agents for cluster headaches.
Mapping global new-onset, worsening, and resolution of diabetes following partial pancreatectomy: a systematic review and meta-analysis
Authors: Wei Junlun , Ou Yiran , Chen Jiaoting , Yu Zhicheng , Wang Zhenghao , Wang Ke , Yang Dujiang , Gao Yun , Liu Yong , Liu Jiaye , Zheng Xiaofeng
Published: December 2023

Background and aims:

Partial pancreatectomy, commonly used for chronic pancreatitis, or pancreatic lesions, has diverse impacts on endocrine and metabolism system. The study aims to determine the global prevalence of new-onset, worsening, and resolution of diabetes following partial pancreatectomy.

Methods:

The authors searched PubMed, Embase, Web of Science, and Cochrane Library from inception to October, 2023. DerSimonian-Laird random-effects model with Logit transformation was used. Sensitivity analysis, meta-regression, and subgroup analysis were employed to investigate determinants of the prevalence of new-onset diabetes.

Results:

A total of 82 studies involving 13 257 patients were included. The overall prevalence of new-onset diabetes after partial pancreatectomy was 17.1%. Univariate meta-regression indicated that study size was the cause of heterogeneity. Multivariable analysis suggested that income of country or area had the highest predictor importance (49.7%). For subgroup analysis, the prevalence of new-onset diabetes varied from 7.6% (France, 95% CI: 4.3–13.0) to 38.0% (UK, 95% CI: 28.2–48.8, P<0.01) across different countries. Patients with surgical indications for chronic pancreatitis exhibited a higher prevalence (30.7%, 95% CI: 21.8–41.3) than those with pancreatic lesions (16.4%, 95% CI: 14.3–18.7, P<0.01). The type of surgical procedure also influenced the prevalence, with distal pancreatectomy having the highest prevalence (23.7%, 95% CI: 22.2–25.3, P<0.01). Moreover, the prevalence of worsening and resolution of preoperative diabetes was 41.1 and 25.8%, respectively.

Conclusions:

Postoperative diabetes has a relatively high prevalence in patients undergoing partial pancreatectomy, which calls for attention and dedicated action from primary care physicians, specialists, and health policy makers alike.
Definition, diagnosis, and treatment of respiratory sarcopenia
Authors: Miyazaki Shinjiro , Tamaki Akira , Wakabayashi Hidetaka , Arai Hidenori
Published: December 2023

Purpose of review

Skeletal muscle weakness and wasting also occurs in the respiratory muscles, called respiratory sarcopenia. Respiratory sarcopenia may lead to worse clinical indicators and outcomes. We present a novel definition and diagnostic criteria for respiratory sarcopenia, summarize recent reports on the association between respiratory sarcopenia, physical and nutritional status, and clinical outcomes, and provide suggestions for the prevention and treatment of respiratory sarcopenia.

Recent findings

Recently, a novel definition and diagnostic criteria for respiratory sarcopenia have been prepared. Respiratory sarcopenia is defined as a condition in which there is both low respiratory muscle strength and low respiratory muscle mass. Respiratory muscle strength, respiratory muscle mass, and appendicular skeletal muscle mass are used to diagnose respiratory sarcopenia. Currently, it is challenging to definitively diagnose respiratory sarcopenia due to the difficulty in accurately determining low respiratory muscle mass. Decreased respiratory muscle strength and respiratory muscle mass are associated with lower physical and nutritional status and poorer clinical outcomes. Exercise interventions, especially respiratory muscle training, nutritional interventions, and their combinations may effectively treat respiratory sarcopenia. Preventive interventions for respiratory sarcopenia are unclear.

The novel definition and diagnostic criteria will contribute to promoting the assessment and intervention of respiratory sarcopenia.
Acute Pancreatitis
Authors: Wiley Mark B. , Mehrotra Kunaal , Bauer Jessica , Yazici Cemal , Bialkowska Agnieszka B. , Jung Barbara
Published: December 2023

Objective

Severe acute pancreatitis (SAP), pancreatic inflammation leading to multiorgan failure, is associated with high morbidity and mortality. There is a critical need to identify novel therapeutic strategies to improve clinical outcomes for SAP patients.

Materials and Methods

A comprehensive literature review was performed to identify current clinical strategies, known molecular pathophysiology, and potential therapeutic targets for SAP.

Results

Current clinical approaches focus on determining which patients will likely develop SAP. However, therapeutic options are limited to supportive care and fluid resuscitation. The application of a novel 5-cytokine panel accurately predicting disease outcomes in SAP suggests that molecular approaches will improve impact of future clinical trials in AP.

Conclusions

Inflammatory outcomes in acute pancreatitis are driven by several unique molecular signals, which compound to promote both local and systemic inflammation. The identification of master cytokine regulators is critical to developing therapeutics, which reduce inflammation through several mechanisms.
Machine Learning of Histopathological Images Predicts Recurrences of Resected Pancreatic Ductal Adenocarcinoma With Adjuvant Treatment
Authors: Yamaguchi Ruri , Morikawa Hiromu , Akatsuka Jun , Numata Yasushi , Noguchi Aya , Kokumai Takashi , Ishida Masaharu , Mizuma Masamichi , Nakagawa Kei , Unno Michiaki , Miyake Akimitsu , Tamiya Gen , Yamamoto Yoichiro , Furukawa Toru
Published: December 2023

Objectives

Pancreatic ductal adenocarcinoma is an intractable disease with frequent recurrence after resection and adjuvant therapy. The present study aimed to clarify whether artificial intelligence–assisted analysis of histopathological images can predict recurrence in patients with pancreatic ductal adenocarcinoma who underwent resection and adjuvant chemotherapy with tegafur/5-chloro-2,4-dihydroxypyridine/potassium oxonate.

Materials and Methods

Eighty-nine patients were enrolled in the study. Machine-learning algorithms were applied to 10-billion-scale pixel data of whole-slide histopathological images to generate key features using multiple deep autoencoders. Areas under the curve were calculated from receiver operating characteristic curves using a support vector machine with key features alone and by combining with clinical data (age and carbohydrate antigen 19-9 and carcinoembryonic antigen levels) for predicting recurrence. Supervised learning with pathological annotations was conducted to determine the significant features for predicting recurrence.

Results

Areas under the curves obtained were 0.73 (95% confidence interval, 0.59–0.87) by the histopathological data analysis and 0.84 (95% confidence interval, 0.73–0.94) by the combinatorial analysis of histopathological data and clinical data. Supervised learning model demonstrated that poor tumor differentiation was significantly associated with recurrence.

Conclusions

Results indicate that machine learning with the integration of artificial intelligence–driven evaluation of histopathological images and conventional clinical data provides relevant prognostic information for patients with pancreatic ductal adenocarcinoma.
Examining the Relationship Between Nurses’ Fear of COVID-19 and Nursing Care Behavior
Authors: Ceylan Burcu , Aktan Gul Gunes , Coskun Palaz Simge
Published: December 2023

Objectives

It is clear that COVID-19, and especially its highly infectious nature, has caused fear, anxiety, and worry for nurses performing active duty during the pandemic. It has thus been a matter of interest to investigate into how care behaviors have been affected by the various emotions that continue to be felt in this period. This study aimed to examine the impact of nurses’ fear of COVID-19 on their nursing care behavior during the pandemic.

Methods

The data of this descriptive and cross-sectional designed study were collected from 450 nurses providing one-on-one care (at university, public, or private hospital) to COVID-19 patients from January to March 2021 and who had consented to participate in the study. A Personal Data Form, the “Caring Behaviors Inventory-24 (CBI-24),” and the “Fear of COVID-19 Scale” were used in the data collection.

Results

The overall mean score of the nurses on the Caring Behaviors Inventory was 5.08 ± 0.59. An examination of the subscales showed that the nurses’ highest scores were in the knowledge and skills subscale, whereas they scored the lowest in the loyalty subscale. The overall mean score of the nurses on the Fear of COVID-19 Scale was 18.52 ± 5.43. A negative, significant, and very weak relationship was found between the nurses’ levels of fear of coronavirus and their care behaviors (r= −0.107,P< 0.05).

Conclusions

Data show that nurses providing care to patients during the COVID-19 pandemic feared COVID-19, that their care behaviors were generally at a good level, and that the care behaviors of nurses with a high degree of fear of COVID-19 were negatively and significantly impacted.
Why Simulation Matters: A Systematic Review on Medical Errors Occurring During Simulated Health Care
Authors: Bokka Leshya , Ciuffo Francesco , Clapper Timothy C.
Published: December 2023

Background

Over the past decade, the implementation of simulation education in health care has increased exponentially. Simulation-based education allows learners to practice patient care in a controlled, psychologically safe environment without the risk of harming a patient. Facilitators may identify medical errors during instruction, aiding in developing targeted education programs leading to improved patient safety. However, medical errors that occur during simulated health care may not be reported broadly in the simulation literature.

Objective

The aim of the study is to identify and categorize the type and frequency of reported medical errors in healthcare simulation.

Methods

Systematic review using search engines, PubMed/MEDLINE, CINAHL, and SCOPUS from 2000 to 2020, using the terms “healthcare simulation” AND “medical error.” Inclusion was based on reported primary research of medical errors occurring during simulated health care. Reported errors were classified as errors of commission, omission, systems related, or communication related.

Results

Of the 1105 articles screened, only 20 articles met inclusion criteria. Errors of commission were the most reported (17/20), followed by systems-related errors (13/20), and errors of omission (12/20). Only 7 articles reported errors attributed to communication. Authors in 16 articles reported more than one type of error.

Conclusions

Simulationists and patient safety advocates must continually identify systems-related errors and training deficits that can lead to inaction, improper action, and poor communication. Recent dialogs in the simulation community have also underscored the potential benefits of developing a registry of errors across simulation centers, with a goal of aggregating, analyzing, and disseminating insights from various simulation exercises.
A NURSING PHILOSOPHY OF MOTIVATIONAL INTERVIEWING ON TYPE 2 DIABETES MELLITUS: SYSTEMATIC REVIEW
Authors: Mumpuningtias Elyk Dwi , Pandin Moses Glorino Rumambo , Nursalam Nursalam
Published: December 2023

Background

The management of Type 2 Diabetes Mellitus (T2DM) heavily relies on lifestyle choices and adherence. Opting for a high-risk lifestyle can exacerbate the impact on individuals with T2DM, worsening their condition. These approaches encompass self-care practices, cognitive behavioral strategies, training for family support, and educational initiatives focusing on lifestyle changes. Motivational interviewing is one strategy to changes behavior of T2DM patients.

Method

This study reviewed the literature following the PRISMA guidelines (2019– 2023). The exploration involved keyword searches for “motivational interviewing,” “T2DM,” “lifestyle,” and “glycemic index” across databases such as Scopus, Science Direct, and ProQuest. Inclusion criteria encompassed quantitative research design, English language publications, research involving patients with T2DM, motivational interviewing, lifestyle modifications, and glycemic index. This resulted in the identification of 286 papers. A PICO synthesis and grouping method was used to analyze the data, aligned with the Cochrane Handbook for Systematic Reviews. The methodological quality assessment, carried out using the Joanna Briggs Institute Critical Appraisal methodology, indicated that adopting a multidisciplinary approach involving ontological, epistemological, and axiological inquiry is a robust foundation for enhancing health information systems and clinical practice.

Results

This study reviewed ten articles focusing on using motivational interviewing techniques to improve T2DM patients so that they can change their lifestyle and manage their glycemic index in the long term. Motivational interviewing can be conducted face to face for an average of 10-12 sessions, approximately3-6 months, both online and through intensive intervention.

Conclusion

This study can demonstrate how motivational interviews can improve the behavior of T2DM patients by changing lifestyle and reducing the glycemic index in T2DM patients.
Dengue virus transmission in Italy: surveillance and epidemiological trends up to 2023
Authors: Branda Francesco , Nakase Taishi , Maruotti Antonello , Scarpa Fabio , Ciccozzi Alessandra , Romano Chiara , Peletto Simone , Bispo de Filippis Ana Maria , Alcantara Luiz Carlos Junior , Marcello Alessandro , Ciccozzi Massimo , Lourenço José , Giovanetti Marta
Published: December 2023

Dengue virus circulation is on the rise globally with increased epidemic activity in previously unaffected countries, including within the European region. In 2023, global dengue activity peaked, and Italy reported the highest number of dengue cases and local chains of transmission to date. By curating several sources of information, we introduce a novel data repository focused on dengue reporting in Italy. We integrate geographic, epidemiological, genomic and climatic spatio-temporal data to present an overview of transmission patterns of the past eight years related to circulating viral lineages, geographic distribution, hotspots of reporting, and the theoretical contribution of local climate. This study contributes to a better understanding of the evolving scenario in Italy, with the potential to inform reassessment and planning of adequate national and European public health strategies to manage the emergence of dengue.
Fractal correlation properties of heart rate variability as a marker of exercise intensity during incremental and constant-speed treadmill running
Authors: van Rassel C. R. , Ajayi O. O. , Sales K. M. , Clermont A. C. , Rummel M. , MacInnis M.J.
Published: December 2023

The short-term scaling exponent of detrended fluctuation analysis (DFAα1) applied to interbeat intervals may provide a method to identify ventilatory thresholds and indicate systemic perturbation during prolonged exercise. The purposes of this study were to i) confirm whether DFAα1 values of 0.75 and 0.5 coincide with the gas exchange threshold (GET) and respiratory compensation point (RCP), ii) quantify DFAα1 during constant-speed running near the maximal lactate steady state (MLSS), and iii) assess the repeatability of DFAα1 between MLSS trials. Seventeen runners performed an incremental running test, and eleven and ten runners also performed constant-speed running 5% below, at, and 5% above the MLSS, and a repeat trial at MLSS, respectively. GET (bias [LOA]: –3.6 [–9.1 to 1.9] mL·kg−1·min−1) and RCP (–3.5 [–14.1 to 7.2] mL·kg−1·min−1) were overestimated using DFAα1. DFAα1 responses during 30-min running trials near MLSS were variable (i.e., 0.27 to 1.24), and affected by intensity (p=0.019) and duration (p=0.001). No difference in DFAα1 was detected between MLSS trials (p=0.926). These results question whether DFAα1 values can accurately delineate exercise thresholds, but the dependency of DFAα1 on intensity and duration support its potential use to quantify systemic perturbations imposed by continuous exercise.
Implementation of Evidence-Based Medicine in Primary Care Through the Use of Encounter Shared Decision Making Tools: The ShareEBM Pragmatic Trial
Authors: LeBlanc Annie , Branda Megan E , Egginton Jason , Inselman Jonathan W , Dick Sara , Schuerman Janet , Kemper Jill , Shah Nilay D , Montori Victor M
Published: December 2023

BACKGROUND

While decision aids have been proven effective to facilitate patient-centered discussion about evidence-based health information in practice and enable shared decision making (SDM), a chasm remains between the promise and the use of these SDM tools in practice.

AIMS

To promote evidence-based patient-centered care in primary care by using encounter SDM tools for medication management of chronic conditions.

METHODS

We conducted a mixed methods study centered around a practice-based, multi-centered pragmatic randomized trial comparing active implementation (active) to passive dissemination (passive) of a web-based toolkit, ShareEBM, to facilitate the uptake in primary care of four SDM tools designed for use during clinical encounters. These tools supported collaborative decisions about medications for chronic conditions. ShareEBM included activities and tactics to increase the likelihood that encounter SDM tools will be routinized in practice. Study team members worked closely with practices in the active arm to actively integrate and promote the use of SDM tools; passive arm practices received no support from the study team. The embedded qualitative evaluation included clinician phone interviews (n=10) and site observations (n=5) for active practices, and exit focus groups for all practices (n=11).

RESULTS

Eleven practices and 62 clinicians participated in the study. Clinicians in the active arm used SDM tools in 621 encounters (Mean [SD]: 21 [25] encounters per clinician, range: 0-93) compared to 680 in the passive arm (Mean [SD]: 20 [40] encounters per clinician, range: 0-156, p=0.4). Six of 29 (21%) clinicians in the active arm and 14 of 33 (42%) in the passive arm did not use any tools (p=0.1). Clinicians’ views covered four major themes: general views of using encounter SDM tools, perceived impact on patients, strategies used, and how encounter SDM tools are incorporated into practice flow.

CONCLUSION

Neither active nor passive implementation of a toolkit improved the uptake and use of encounter SDM tools in primary care. Overcoming clinician reluctance to consider using encounter SDM tools, their seamless integration into the electronic and practice workflows, and ongoing feedback about the quality of their use during encounters appear necessary to implement their use in primary care practices.
RAPID RESISTANCE TO BET INHIBITORS IS MEDIATED BY FGFR1 IN GLIOBLASTOMA
Authors: Jermakowicz Anna M. , Kurimchak Alison M. , Johnson Katherine J. , Bourgain-Guglielmetti Florence , Kaeppeli Simon , Affer Maurizio , Pradhyumnan Hari , Suter Robert , Walters Winston , Cepero Maria , Duncan James , Ayad Nagi G.
Published: December 2023

Bromodomain and extra-terminal domain (BET) proteins are therapeutic targets in several cancers including the most common malignant adult brain tumor glioblastoma (GBM). Multiple small molecule inhibitors of BET proteins have been utilized in preclinical and clinical studies. Unfortunately, BET inhibitors have not shown efficacy in clinical trials enrolling GBM patients. One possible reason for this may stem from resistance mechanisms that arise after prolonged treatment within a clinical setting. However, the mechanisms and timeframe of resistance to BET inhibitors in GBM is not known. To identify the temporal order of resistance mechanisms in GBM we performed quantitative proteomics using multiplex-inhibitor bead mass spectrometry and demonstrated that intrinsic resistance to BET inhibitors in GBM treatment occurs rapidly within hours and involves the fibroblast growth factor receptor 1 (FGFR1) protein. Additionally, small molecule inhibition of BET proteins and FGFR1 simultaneously induces synergy in reducing GBM tumor growthin vitroandin vivo. Further, FGFR1 knockdown synergizes with BET inhibitor mediated reduction of GBM cell proliferation. Collectively, our studies suggest that co-targeting BET and FGFR1 may dampen resistance mechanisms to yield a clinical response in GBM.
Gut microbiota influences foraging onset without affecting division of labor and associated physiological hallmarks in honeybees
Authors: Liberti Joanito , Frank Erik T. , Kay Tomas , Kesner Lucie , Monié--Ibanes Maverick , Quinn Andrew , Schmitt Thomas , Keller Laurent , Engel Philipp
Published: December 2023

Gut microbes can impact cognition and behavior, but whether they regulate division of labor in animal societies is unknown. We addressed this question using honeybees since they exhibit division of labor between nurses and foragers and because their gut microbiota can be manipulated. Using automated behavioral tracking and controlling for co-housing effects, we show that gut microbes influence the age at which bees start foraging but have no effects on the time spent in a foraging area and number of foraging trips. Moreover, the gut microbiota did not influence hallmarks of behavioral maturation such as body weight, cuticular hydrocarbon (CHC) profile, hypopharyngeal gland size, and the proportion of bees maturing into foragers. Overall, this study shows that the honeybee gut microbiota does not affect division of labor but rather plays an important function in controlling the onset of bee foraging.
Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others
Authors: Gilbert Donald G.
Published: December 2023

Significant discrepancies in genome sizes measured by cytometric methods versus DNA sequence estimates are frequent, including recent long-read DNA assemblies of plant and animal genomes. A new DNA sequence measure using a baseline of unique conserved genes, Gnodes, finds the larger cytometric measures are often accurate. DNA-informatic measures of size, as well as assembly methods, have errors in methodology that under-measure duplicated genome spans.

Major contents of several model and discrepant genomes are assessed here, including human, corn, chicken, insects, crustaceans, and the model plant. Transposons dominate larger genomes, structural repeats are often a major portion of smaller ones. Gene coding sequences are found in similar amounts across the taxonomic spread. The largest contributors to size discrepancies are higher-order repeats, but duplicated coding sequences are a significant missed content, and transposons in some examined species.

Informatics of measuring DNA and producing assemblies, including recent long-read telomere to telomere approaches, are subject to mistakes in operation and/or interpretation that are biased against repeats and duplications. Mistaken aspects include alignment methods that are inaccurate for high-copy duplicated spans; misclassification of true repetitive sequence as heterozygosity and artifact; software default settings that exclude high-copy DNA; and overly conservative data processing that reduces duplicated genomic spans. Re-assemblies with balanced methods recover the missing portions of problem genomes including model plant, water fleas and fire ant.
Single cell transcriptomics reveals chondrocyte differentiation dynamicsin vivoandin vitro
Authors: Lawrence John E G , Woods Steven , Roberts Kenny , Sumanaweera Dinithi , Balogh Petra , Predeus Alexander V , He Peng , Li Tong , Polanski Krzysztof , Prigmore Elena , Tuck Elizabeth , Mamanova Lira , Zhou Di , Webb Simone , Jardine Laura , He Xiaoling , Barker Roger A , Haniffa Muzlifah , Flanagan Adrienne M , Young Matthew D , Behjati Sam , Bayraktar Omer , Kimber Susan J , Teichmann Sarah A
Published: December 2023

The consistent production ofin vitrochondrocytes that faithfully recapitulatein vivodevelopment would be of great benefit for musculoskeletal disease modelling and regenerative medicine. Current efforts are often limited by off-target differentiation, resulting in a heterogeneous product. Furthermore, the lack of comparison to human embryonic tissue, precludes detailed evaluation ofin vitrocells. Here, we perform single-cell RNA sequencing of embryonic long bones dissected from first trimester hind limbs from a range of gestational ages. We combine this with publicly available data to form a detailed atlas of endochondral ossification, which we then use to evaluate a series of publishedin vitrochondrogenesis protocols, finding substantial variability in cell states produced by each. We apply single-nuclear RNA sequencing to one protocol to enable direct comparison betweenin vitroandin vivo,and perform trajectory alignment between the two to reveal differentiation dynamics at the single-cell level, shedding new light on off-target differentiationin vitro. Using this information, we inhibit the activity of FOXO1, a transcription factor predicted to be active in embryonic bone development and in chondrogenic cellsin vitro, and increase chondrocyte transcriptsin vitro.This study therefore presents a new framework for evaluating tissue engineering protocols, using single-cell data from human development to drive improvement and bring the prospect of true engineered cartilage closer to reality.
Inactivation of p53 drives breast cancer brain metastasis by altering fatty acid metabolism
Authors: Laue Kathrin , Pozzi Sabina , Cohen-Sharir Yael , Winkler Tom , Eliezer Yonatan , Israeli Dangoor Sahar , Leikin-Frenkel Alicia I. , Lange Katharina , Zerbib Johanna , Ricci Alessia A. , Sacconi Andrea , Berthelet Jean , Schäffer Alexander , Shi Wei , Liao Yang , Barshack Iris , Medyouf Hind , Merino Delphine , Blandino Giovanni , Bertero Luca , Satchi-Fainaro Ronit , Ben-David Uri
Published: December 2023

Brain metastasis (BM) is a dire prognosis across cancer types. It is largely unknown why some tumors metastasize to the brain whereas others do not. We analyzed genomic and transcriptional data from clinical samples of breast cancer BM (BCBM) and found that nearly all of them carried p53-inactivating genetic alterations through mutations, copy-number loss, or both. Importantly, p53 pathway activity was already perturbed in primary tumors giving rise to BCBM, often by loss of the entire 17p chromosome-arm. This association was recapitulated across other carcinomas. Experimentally, p53 knockout was sufficient to drastically increase BCBM formation and growthin vivo, providing a causal link between p53 inactivation and brain tropism. Mechanistically, p53-deficient BC cells exhibited altered lipid metabolism, particularly increased fatty acid (FA) synthesis and uptake, which are characteristic of brain-metastasizing cancer cells. FA metabolism was further enhanced by astrocytes in a p53-dependent manner, as astrocyte-conditioned medium increased FASN, SCD1, and CD36 expression and activity, and enhanced the survival, proliferation and migration of p53-deficient cancer cells. Consequently, these cells were more sensitive than p53-competent cells to FA synthesis inhibitors, in isogenic cell cultures, in BCBM-derived spheroids, and across dozens of BC cell lines. Lastly, a significant association was observed between p53 inactivation, astrocyte infiltration, and SCD1 expression in clinical human BCBM samples. In summary, our study identifies p53 inactivation as a driver of BCBM and potentially of BM in general; suggests a p53-dependent effect of astrocytes on BC cell behavior; and reveals FA metabolism as an underlying, therapeutically-targetable molecular mechanism.
Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19
Authors: Lee Jimmy Tsz Hang , Barnett Sam N. , Roberts Kenny , Ashwin Helen , Milross Luke , Cho Jae-Won , Huseynov Alik , Woodhams Benjamin , Aivazidis Alexander , Li Tong , Majo Joaquim , Guerrero Patricia Chaves , Lee Michael , Miranda Antonio M. A. , Jablonska Zuzanna , Arena Vincenzo , Hanley Brian , Osborn Michael , Uhlmann Virginie , Xu Xiao-Ning , McLean Gary R , Teichmann Sarah A. , Randi Anna M. , Filby Andrew , Kaye Paul M. , Fisher Andrew J. , Hemberg Martin , Noseda Michela , Bayraktar Omer Ali
Published: December 2023

The most common cause of death due to COVID-19 remains respiratory failure. Yet, our understanding of the precise cellular and molecular changes underlying lung alveolar damage is limited. Here, we integrate single cell transcriptomic data of COVID-19 donor lungs with spatial transcriptomic data stratifying histopathological stages of diffuse alveolar damage (DAD). We identify changes in cellular composition across progressive DAD, including waves of molecularly distinct macrophages and depleted epithelial and endothelial populations throughout different types of tissue damage. Predicted markers of pathological states identify immunoregulatory signatures, including IFN-alpha and metallothionein signatures in early DAD, and fibrosis-related collagens in organised DAD. Furthermore, we predict a fibrinolytic shutdown via endothelial upregulation ofSERPINE1/PAI-1. Cell-cell interaction analysis revealed macrophage-derivedSPP1/osteopontin signalling as a key regulator during early DAD. These results provide the first comprehensive, spatially resolved atlas of DAD stages, highlighting the cellular mechanisms underlying pro-inflammatory and pro-fibrotic pathways across alveolar damage progression.
Exploration of the intricacies of low light-induced changes in cigar tobacco leaf anticlinal growth: A holistic approach from anatomical and hormonal levels to gene expression
Authors: Ma Xinghua , Yang Jinpeng , Ren Xiaochun , Chen Keling , Yang Chunlei , Gao Huajun , Khan Rayyan
Published: December 2023

Cigar tobacco stands as a pivotal economic crop, with its leaf growth and development profoundly influenced by light intensity. It specifically aims to investigate how leaf morphology and anticlinal growth respond to varying light intensities, including normal light intensity (NL–300 μmol m−2s−1) and lower light intensity (LL–100 μmol m−2s−1). The research elucidates significant morphological shifts in cigar tobacco leaves under LL, revealing notable alterations in leaf area, leaf length, and leaf width. Early reductions in leaf dimensions, ranging from 30% to 48%, were succeeded by a substantial enhancement in expansion rates from day 9 to day 26, contributing to expanded leaf surfaces at later stages. Upper epidermis thickness declined by 29-19%, with a notably slower expansion rate in the initial 20 days. Palisade cell length consistently decreased by 52-17%, corresponding with upper epidermis trends. Spongy tissue thickness was reduced by 31-12%, with a slower expansion rate in LL for the initial 14 days, and leaf thickness dropped by 34-11%. LL resulted in slower leaf anticlinal expansion, leading to reduced leaf thickness (LT). LL significantly influenced phytohormones in cigar tobacco leaves. Gibberellic acid (41% to 16%) and auxin (20% to 35%) levels were found in higher amounts, while cytokinin levels (19% to 5%) were lowered compared to NL, indicating the intricate regulatory role of light in hormonal dynamics. The observed increase in LT and different cell layers at specific time points (day 8, day 12, day 24, and day 28) under LL, although lower than NL, may be attributed to elevated expression of genes related to cell expansion, includingGRF1,XTH, andSAUR19at those time points. This comprehensive understanding elucidates the intricate mechanisms by which light intensity orchestrates the multifaceted processes governing leaf anatomy and anticlinal expansion in cigar tobacco plants.
Hepatitis B virus neutralization with DNA origami nanoshells
Authors: Willner Elena M. , Kolbe Fenna , Momburg Frank , Protzer Ulrike , Dietz Hendrik
Published: December 2023

We demonstrate the use of DNA origami to create virus-trapping nanoshells that efficiently neutralize hepatitis B virus (HBV) in cell culture. By modifying the shells with a synthetic monoclonal antibody that binds to theHBVenvelope, the effective neutralization potency per antibody is increased by approximately 100 times compared to using free antibodies. The improvements in neutralizing the virus are attributed to two factors: first, the shells act as a physical barrier that block the virus from interacting with host cells; second, the multivalent binding of the antibodies inside the shells lead to stronger attachment to the trapped virus, a phenomenon known as avidity. Pre-incubation of shells withHBVand simultaneous addition of both components separately to cells lead to comparable levels of neutralization, indicating rapid trapping of the virions by the shells. Our study highlights the potential of the DNA shell system to rationally create novel antivirals using components that, when used individually, show little to no antiviral effectiveness.
A common druggable signature of oncogenic CMYC, mutant KRAS and mutant p53 reveals functional redundancy and competition of the oncogenes in cancer
Authors: Grześ Maria , Jaiswar Akanksha , Grochowski Marcin , Wojtyś Weronika , Kaźmierczak Wojciech , Olesiński Tomasz , Lenarcik Małgorzata , Nowak-Niezgoda Magdalena , Kołos Małgorzata , Canarutto Giulia , Piazza Silvano , Wiśniewski Jacek R. , Walerych Dawid
Published: December 2023

Major driver oncogenesCMYC, mutantKRAS and mutantTP53often co-exist and cooperate in promoting human neoplasia. By CRISPR-Cas9-mediated downregulation we determined their proteomics and transcriptomics downstream programs in a panel of cell lines with activated either single or three oncogenes – in cancers of lung, colon and pancreas. This allowed to define and screen the oncogenes’ common functional program for anti-cancer target candidates, and find protocols which efficiently kill cancer cells and organoids by targeting pathways represented by a signature of three genes:RUVBL1, HSPA9andXPO1. We found that these genes were controlled by the driver oncoproteins in a redundant or competitive manner, rather than by cooperation. Each oncoprotein individually was able to upregulate the three target genes, while upon oncogene co-expression each target was controlled preferably by a specific oncoprotein which reduced the influence of the others. Mechanistically this redundancy was mediated by parallel routes of the target gene activation – as in the case of mutant KRAS signaling to C-JUN and GLI-2 transcription factors bypassing CMYC, and by competition – as in the case of mutant p53 and CMYC competing for biding to the target promoters. The transcriptomics data from the cell lines and patient samples indicate that the redundancy of the oncogenic programs is a broad phenomenon which may comprise even a majority of the genes dependent on the oncoprotein, as shown for mutant p53 in colon and lung cancer cell lines. Nevertheless, we demonstrate that the redundant oncogene programs harbor targets of efficient anti-cancer drug combinations, bypassing limitations of a direct oncoprotein inhibition.
The developing pig respiratory microbiome harbours strains antagonistic to common respiratory pathogens
Authors: Vlasblom Abel A. , Duim Birgitta , Patel Shriram , Luiken Roosmarijn E. C. , Crespo-Piazuelo Daniel , Eckenberger Julia , Huseyin Chloe E. , Lawlor Peadar G. , Elend Christian , Wagenaar Jaap A. , Claesson Marcus J. , Zomer Aldert L.
Published: December 2023

In the global efforts to combat antimicrobial resistance and reduce antimicrobial use in pig production, there is a continuous search for methods to prevent and/or treat infections. Within this scope, we explored the relationship between the developing piglet nasal microbiome and (zoonotic) bacterial pathogens from birth until ten weeks of life. The nasal microbiome of 54 pigs was longitudinally studied over 16 time-points on nine farms in three European countries (Germany, Ireland, and the Netherlands) using amplicon sequencing targeting the V3-V4 16S rRNA region as well as thetufgene for itsStaphylococcaldiscrimination power. The piglets’ age, the farm, and the litter affected the nasal microbiome, with piglets’ age explaining 19% of the variation in microbial composition between samples. Stabilization of the microbiome occurred around two weeks post-weaning. Notably, while opportunistic pathogens were ubiquitously present, they did not cause disease. The piglet nasal microbiome often carried species associated with gut, skin, or vagina, which suggests that contact with the vaginal and faecal microbiomes shape the piglet nasal microbiome. We identified bacterial Co-Abundance Groups (CAGs) of species that were present in the nasal microbiomes in all three countries over time. Anticorrelation between these species and known bacterial pathogens identified strains that might be exploited for pathogen reduction. Further experimental evidence is required to confirm these findings. Overall, this study advances our understanding of the longitudinal development and factors influencing the piglet nasal microbiome, providing insights into its role in health and disease.

Importance

Our study on longitudinal analysis of the developing nasal microbiota of piglets in farms in three European countries showed consistent microbiome compositions and that colonization of porcine pathogens occurred in relation with anticorrelating species. These findings enhance our knowledge of co-colonizing species in the nasal cavity, and the identified microbial interactions can be explored for the development of interventions to control pathogens in porcine husbandry.
High Resolution Outdoor Videography of Insects Using Fast Lock-On Tracking
Authors: Vo-Doan T. Thang , Titov Victor V. , Harrap Michael J.M. , Lochner Stephan , Straw Andrew D.
Published: December 2023

Insects have significant global impacts on ecology, economy, and health and yet our understanding of their behavior remains limited. Bees, for example, use vision and a tiny brain to find flowers and return home, but understanding how they perform these impressive tasks has been hampered by limitations in recording technology. Here we present Fast Lock-On (FLO) tracking. This method moves an image sensor to remain focused on a retroreflective marker affixed to an insect. Using paraxial infrared illumination, simple image processing can localize the sensor location of the insect in a few milliseconds. When coupled with a feedback system to steer a high magnification optical system to remain focused on the insect, a high spatial-temporal resolution trajectory can be gathered over a large region. As the basis for several robotic systems, we show FLO is a versatile idea which can be employed in combination with other components. We demonstrate that the optical path can be split and used for recording high-speed video. Furthermore, by flying a FLO system on a quadcopter drone, we track a flying honey bee and anticipate tracking insects in the wild over kilometer scales. Such systems have the capability of providing higher resolution information about insects behaving in natural environments and as such will be helpful in revealing the biomechanical and neuroethological mechanisms used by insects in natural settings.

One-Sentence Summary

Fast Lock-On tracking enables recording trajectories and high-speed videos of insects behaving over large areas in the wild.
Horizontal transfer and recombination fuel Ty4 retrotransposon evolution inSaccharomyces
Authors: Chen Jingxuan , Garfinkel David J. , Bergman Casey M.
Published: December 2023

Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely-related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genusSaccharomycesusing short- and long-read whole genome sequence data, including new PacBio genome assemblies for twoS. mikataestrains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages ofS. paradoxus,S. cerevisiae,S. eubayanus,S. kudriavzeviiand the ancestor of theS. mikatae/S. jureispecies pair. In bothS. mikataeandS. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally-transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genusSaccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon cladesviarecombination.
Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates
Authors: Rossio Valentina , Paulo Joao A. , Liu Xinyue , Gygi Steven P. , King Randall W.
Published: December 2023

Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs inXenopusegg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high impact DUBs (USP7, USP9X, USP36, USP15 and USP24) that each reduced ubiquitylation of over ten percent of the isolated proteins. Candidate substrates of high impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.