bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of continued alcohol use on liver-related outcomes of alcohol-associated cirrhosis: a retrospective study of 440 patients
Authors: Kalambokis Georgios N. , Chouliara Nikolleta , Tsiakas Ilias , Filippas-Ntekuan Sempastien , Christaki Maria , Despotis Grigorios , Milionis Haralampos
Published: October 2023

Background and aim

The prevalence of alcohol-associated cirrhosis is increasing. In this respect, we investigated the long-term impact of non-abstinence on the clinical course of alcohol-associated cirrhosis.

Methods

We retrospectively evaluated 440 patients with alcohol-associated cirrhosis (compensated cirrhosis: n = 190; decompensated cirrhosis: n = 250) diagnosed between January 2000 and July 2017 who consumed alcohol until diagnosis of cirrhosis. We assessed liver-related outcomes including first and further decompensating events (ascites, variceal bleeding, and hepatic encephalopathy), and death in relation to continued alcohol use.

Results

Overall, 53.6% of patients remained abstinent (compensated cirrhosis: 57.9%; decompensated cirrhosis: 50.4%). Non-abstinent versus abstinent patients with compensated cirrhosis and decompensated cirrhosis showed significantly higher 5-year probability of first decompensation (80.2% vs. 36.8%; P < 0.001) and further decompensation (87.9% vs. 20.6%; P < 0.001), respectively. Five-year survival was substantially lower among non-abstinent patients with compensated cirrhosis (45.9% vs. 90.7%; P < 0.001) and decompensated cirrhosis (22.9% vs. 73.8%; P < 0.001) compared to abstinent. Non-abstinent versus abstinent patients of the total cohort showed an exceedingly lower 5-year survival (32.2% vs. 82.4%; P < 0.001). Prolonged abstinence (≥2 years) was required to influence outcomes. Non-abstinence independently predicted mortality in the total cohort (hazard ratio [HR] 3.371; confidence interval [CI]: 2.388–4.882; P < 0.001) along with the Child-Pugh class (HR: 4.453; CI: 2.907–6.823; P < 0.001) and higher age (HR: 1.023; CI: 1.007–1.039; P = 0.005).

Conclusion

Liver-related outcomes are worse among non-abstinent patients with alcohol- associated cirrhosis prompting urgent interventions ensuring abstinence.
Stress-only versus rest-stress SPECT MPI in the detection and diagnosis of myocardial ischemia and infarction by machine learning
Authors: Wang Fanghu , Yuan Hui , Lv Jieqin , Han Xu , Zhou Zidong , Lu Wantong , Lu Lijun , Jiang Lei
Published: October 2023

Background

Rest-stress SPECT myocardial perfusion imaging (MPI) is widely used to evaluate coronary artery disease (CAD). We aim to evaluate stress-only versus rest-stress MPI in diagnosing CAD by machine learning (ML).

Methods

A total of 276 patients with suspected CAD were randomly divided into training (184 patients) and validation (92 patients) cohorts. Variables extracted from clinical, physiological, and rest-stress SPECT MPI were screened. Stress-only and rest-stress MPI using ML were established and compared using the training cohort. Then the diagnostic performance of two models in diagnosing myocardial ischemia and infarction was evaluated in the validation cohort.

Results

Six ML models based on stress-only MPI selected summed stress score, summed wall thickness score of stress%, and end-diastolic volume of stress as key variables and performed equally good as rest-stress MPI in detecting CAD [area under the curve (AUC): 0.863 versus 0.877, P = 0.519]. Furthermore, stress-only MPI showed a reasonable prediction of reversible deficit, as shown by rest-stress MPI (AUC: 0.861). Subsequently, nomogram models using the above-stated stress-only MPI variables showed a good prediction of CAD and reversible perfusion deficit in training and validation cohorts.

Conclusion

Stress-only MPI demonstrated similar diagnostic performance compared with rest-stress MPI using 6 ML algorithms. Stress-only MPI with ML models can diagnose CAD and predict ischemia from scar.
Chronic pelvic pain; more than just the bladder
Authors: Messelink Bert , Flink Ida , dos Santos Ana , Adamse Corine
Published: October 2023

Purpose of review

Chronic pelvic pain is much of a burden to those who suffer from it. Additionally, in many patients medical doctors, such as urologists are unable to identify a cause or clear pathology that can explain the pain. Still numerous patients and doctors keep on searching for a cause, focussing particularly on the pelvic organs. Lots of diagnostics and treatment methods are used but often without success. In recent years, we have gained increased insight into the mechanisms of pain and adapted the terminology accordingly.

Recent findings

Two aspects of chronic pelvic pain have gained more attention. First, the myofascial aspects, especially the role of the pelvic floor muscles in maintaining the pain and as a therapeutic option. Second, the role of the brain and the psychological aspects intertwine with the pain and its consequences also open up for alternative management options. In terminology chronic pain is now included in the ICD-11, a historical change. Introducing chronic primary pain (no cause found) helps us to look away from the organ and deal with the patient as a whole human being.

The findings reported here are helpful for your daily practice. Looking from a broad perspective gives the patient the feeling of being seen and heard. Working together in a multidisciplinary team makes your work easier and gives more satisfaction.

Video abstract

http://links.lww.com/COU/A44
Candida krusei pneumonia in graft-versus-host disease after allogeneic hematopoietic stem cell transplant for paroxysmal nocturnal hemoglobinuria: a case report
Authors: Zoowa Ronit , Shah Ravi , Pradhan Dipana , Karmacharya Sammridhi , Bhandari Dipen
Published: October 2023

Introduction and importance:

Paroxysmal nocturnal hemoglobinuria (PNH) is a rare disorder caused by a somatic mutation of PIGA (phosphatidylinositol glycan anchor biosynthesis, class A) gene that leads to the destruction of blood cells. Allogeneic haematopoietic stem cell transplant (HSCT) is a treatment option for PHN, but it can cause graft-versus-host disease (GVHD). Long-term immunosuppression as a treatment of GVHD increases the risk for invasive fungal infections such as Candida krusei pneumonia.

Case presentation:

We present the case of a 22-year-old male with C. krusei pneumonia in a known case of chronic GVHD following HSCT for PNH undergoing long-term immunosuppressive therapy. The patient presented with progressive shortness of breath, productive cough, palpitations, and difficulty swallowing. On examination, he had skin rashes and oral lesions, along with signs of severe malnutrition. Diagnosis was made on the basis of radiological imaging and fungal culture.

Discussion:

The combination of PNH, GVHD, and HSCT created an immunocompromised state, making the patient susceptible to opportunistic infections, including fungal pneumonia. Early recognition of this condition is challenging due to its non-specific symptoms and potential overlap with other post-transplant complications. Timely diagnosis and appropriate treatment, including antifungal therapy and immunosuppression management, are crucial for optimising patient outcomes.

Conclusion:

This case highlights the importance of early recognition and timely treatment of fungal infections in patients with severe conditions such as GVHD following HSCT for PNH. Timely treatment with appropriate antifungals is necessary for optimal outcomes. Additionally, more research with long-term follow-up and monitoring is necessary to address the necessary knowledge gaps in this field.
A Rapid Review of the Role of Virtual Reality in Care Delivery of Palliative Care and Hospice
Authors: Moutogiannis Panagiota P. , Thrift Jason , Pope J. Keais , Browning Matthew H.E.M. , McAnirlin Olivia , Fasolino Tracy
Published: October 2023

Virtual reality (VR) is an emerging technology that can provide a nonpharmacological approach to symptom management for those with serious illnesses. The VR platform offers a unique perspective to connect patients with places and experiences they might otherwise miss. This rapid review aims to present the current literature on the uses and benefits of VR for palliative care and hospice patients. Through a systematic process, we identified 14 articles published between 2018 and 2023 that used VR as an interventional strategy for symptom management. The VR equipment includes a head-mounted display, such as the Oculus Go, and sometimes requires hand controllers or joysticks. Virtual reality software was contained exclusively in the head-mounted displays or required a laptop. Nature scenes, memorable locations, and the solar system are examples of options patients could select for the VR experience. Assessments of the intervention were measured before, during, after, and several hours afterward to evaluate benefits and potential adverse effects. Pain was the predominant symptom assessed in the studies. Overall, most of the studies focused on establishing the safety, efficacy, and feasibility of VR using a single-arm interventional method. Future research should implement randomized controlled trials, increase sample size, and expand to pediatric populations.
Improving End-of-Life Care for Nursing Home Residents Using an Interprofessional Approach
Authors: Burokas Steven , Parker Susan , Sirard Cherie
Published: October 2023

Interprofessional collaboration enhances quality end-of-life care leading to a dignified death. Hospice care uses an interdisciplinary approach to optimize quality of life and mitigate impacts of serious illness. Interventions to improve hospice care delivery have been proven to be effective, but little is known about nursing home staff preparedness, implementation of hospice education, and interprofessional communication. Research is limited on how hospice care can be implemented into the nursing home setting. The purpose of this study was to determine if education combined with a communication tool improved nursing home staff knowledge and improved communication with the hospice team. The descriptive study invited participants to take a preseminar and postseminar survey to assess end-of-life preparedness in terms of willingness, capability, and resilience. A communication tool was implemented to measure collaboration with the hospice team over 3 months. The results from this study suggest education combined with interprofessional communication improves end-of-life care.
The Gratitude Campaign
Authors: Kelly Lesly A. , Miller Beth A. , Graber Amy , Tran Amanda , Collins Jennifer
Published: October 2023

Nurse well-being and optimism were tested in the midst of COVID-19 patient surges and staffing challenges. Using the American Nurses Foundation Gratitude Toolkit, a health system implemented monthly gratitude practices at 4 hospitals. Validated survey measures indicated that nurses' scores of self-perceived gratitude, flourishing behaviors, and mindfulness were maintained during this challenging time but did not statistically increase. Although statistical significance increases were not demonstrated, the gratitude campaign offered clinical significance through positive feedback and was sustained through the distribution of a toolkit disseminated across the health system.
Advanced Practice RN Student Practicum Placements
Authors: Lofgren Maria , Dunn Heather , Gust Christine , Melsa Worrell Angela , Dirks Mary
Published: October 2023

Academic health centers are faced with limited resources to navigate placement of advanced practice RN (APRN) students at the same time as APRN programs continue to increase. Clinical practicum sites are in higher demand due to clinical hour increases by accrediting organizations. This article describes a successful approach to the inefficient use of administration and preceptor resources for APRN student practicum placements via an innovative academic health system partnership.
The use of Titanium Meshes in Surgical Closure of the Oroantral Fistula. A Randomized Clinical Trial Study
Authors: Tabrizi Reza , Akhlaghi Fahimeh , Javaheri Pouria , Malekigorji Mohsen
Published: October 2023

The closure of oroantral communications (OACs) is challenging. The study aimed to assess the effect of titanium meshes in the outcome of OAC closure by local flaps.

This is a prospective randomized, nonblinded clinical trial. Patients with a delay and large (≥7 mm2) OAC were studied. Patients were randomly divided into 2 groups: in group 1, patients underwent OAC closure through a modified Rehrmann buccal advancement flap with a titanium mesh, and in group 2, the modified Rehrmann buccal advancement flap. The primary predictive factor was the use of titanium mesh. Dehiscence (the breakdown of the edge of flaps without the complete reopening of the defect) was a primary outcome. The defect’s reopening was considered a secondary outcome.

Nineteen patients in group 1 and 20 in group 2 were studied. In 2 months after treatments, the prevalence of dehiscence in group 1 was 3, and 10 patients in group 2 (P=0.041). In group 1, patients did not show OAC exposure. However, OAC exposure was observed in 2 patients in group 2.

This study demonstrates that using titanium mesh in combination with a modified Rehman flap decreases the prevalence of dehiscence compared with a flap alone.
Characterization of two novel Fe(III)-reducing and electrogenic bacteria, Shewanella ferrihydritica sp. nov. and Shewanella electrica sp. nov., isolated from mangrove sediment
Authors: Yao Sijie , Zhang Xueying , Lin Annian , Xia Xue , Lin Lijun , Yang Guiqin , Zhuang Li
Published: October 2023

Three novel strains in the genus

Shewanella

, designated A3AT, C31T and C32, were isolated from mangrove sediment samples. They were facultative anaerobic, Gram-stain-negative, rod-shaped, flagellum-harbouring, oxidase- and catalase-positive, electrogenic and capable of using Fe(III) as an electron acceptor during anaerobic growth. Results of phylogenetic analysis based on 16S rRNA gene and genomic sequences revealed that the strains should be assigned to the genus

Shewanella

. The 16S rRNA gene similarity, average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the isolates and their closely related species were below the respective cut-off values for species differentiation. The 16S rRNA gene similarity, ANI and dDDH values between strains C31T and C32 were 99.7, 99.9 and 99.9 %, respectively, indicating that they should belong to the same genospecies. Based on polyphasic taxonomic approach, two novel species are proposed, Shewanella ferrihydritica sp. nov. with type strain A3AT (GDMCC 1.2732T=JCM 34899T) and Shewanella electrica sp. nov. with type strain C31T (GDMCC 1.2736T=JCM 34902T).
PCLAF-DREAM Drives Alveolar Cell Plasticity for Lung Regeneration
Authors: Kim Bongjun , Huang Yuanjian , Ko Kyung-Pil , Zhang Shengzhe , Zou Gengyi , Zhang Jie , Kim Moon Jong , Little Danielle , Ellis Lisandra Vila , Paschini Margherita , Jun Sohee , Park Kwon-Sik , Chen Jichao , Kim Carla , Park Jae-Il
Published: October 2023

Spatiotemporal control of stem and progenitor cells is essential for lung regeneration, the failure of which leads to lung disease. However, the mechanism of alveolar cell plasticity during regeneration remains elusive. We previously found that PCLAF remodels the DREAM complex for cell cycle re-entry. PCLAF expression is specifically enriched in proliferating lung progenitor cells, along with the DREAM target genes by lung damage. Genetic ablation ofPclafinhibited alveolar type I (AT1) cell regeneration from alveolar type II (AT2) cells, inducing lung fibrosis. Mechanistically, the PCLAF-DREAM complex directly transactivatesCLIC4, promoting TGF-β signaling that regulates the balance between AT1 and AT2 cells. Furthermore, a drug candidate that mimics the PCLAF-DREAM transcriptional signatures for lung regeneration was identified and validated in organoids and mice. Our study unveils an unexpected role of the PCLAF-DREAM axis in controlling alveolar cell plasticity for lung regeneration and proposes a viable option for lung fibrosis prevention.

One Sentence Summary

PCLAF-DREAM-driven alveolar cell plasticity is crucial for lung regeneration and can be pharmacologically targeted as a therapeutic strategy for lung fibrosis.
OxPhos in adipose tissue macrophages regulated by BTK enhances their M2-like phenotype and confers a systemic immunometabolic benefit in obesity
Authors: Purvis Gareth S. D. , Collino Massimo , van Dam Andrea D. , Einaudi Giacomo , Ng Yujung , Shanmuganathan Mayooran ,   Oxford Acute Myocardial Infarction (OxAMI) Study, Patel Smita Y. , Thiemermann Christoph , Channon Keith M. , Greaves David R.
Published: October 2023

Bruton’s tyrosine kinase (BTK) is a non-receptor bound kinase involved in pro-inflammatory signalling in activated macrophages, however, its role within adipose tissue macrophages remains unclear. We have demonstrated that BTK signalling regulates macrophage M2-like polarisation state by up-regulating subunits of mitochondrially encoded electron transport chain Complex I (ND4andNDL4) and Complex IV (mt-CO1,mt-CO2andmt-CO3) resulting in an enhanced rate of oxidative phosphorylation (OxPhos) in an NF-κB independent manner. Critically, BTK expression is elevated in adipose tissue macrophages from obese individuals with diabetes, while key mitochondrial genes (mtC01, mtC02 and mtC03) are decreased in inflammatory myeloid cells from obese individuals. Inhibition of BTK signalling either globally (Xid mice) or in myeloid cells (LysMCreBTK), or therapeutically (Acalabrutinib) protects HFD-fed mice from developing glycaemic dysregulation by improving signalling through the IRS1/Akt/GSK3b pathway. The beneficial effects of acalabrutinib treatment are lost in macrophage ablated mice. Inhibition of BTK signalling in myeloid cells but not B-cells, induced a phenotypic switch in adipose tissue macrophages from a pro-inflammatory M1-state to a pro-resolution M2-like phenotype, by shifting macrophage metabolism towards OxPhos. This reduces both local and systemic inflammation and protects mice from the immunometabolic consequences of obesity. Therefore, in BTK we have identified a macrophage specific, druggable target that can regulate adipose tissue polarisation and cellular metabolism that can confer systematic benefit in metabolic syndrome.

Article high lights

Obesity and diabetes are associated with inflammation, particularly within the adipose tissue. We have found a new druggable target called Bruton’s tyrosine kinase (BTK) that is highly expressed in adipose tissue macrophages. When BTK is inhibited in macrophages, it allows these cells to undergo a phenotypic switch towards an M2-like pro-resolution macrophage. This achieved by increasing expression of key mitochondrially encoded components of the electron transport chain allowing for enhanced OxPhos. Inhibition of BTK signalling in myeloid cells but not B-cells protects HFD-fed mice from developing glycaemic dysregulation.
First record of Zaprionus tuberculatus (Diptera: Drosophilidae) in mainland France
Authors: Georges Romain , Yassin Amir , Colinet Hervé
Published: October 2023

BACKGROUND

As most drosophilid species are not considered as primary pest, studies of the whole drosophilid communities, including other genera thanDrosophila, with standardized surveys are relatively sparse. However, the spotted wing drosophilaDrosophila suzukii(Matsumura, 1931) and its rapid expansion through the world led to the implementation of many monitoring programs in various countries. As part of a research project onD. suzukii, we set up in 2022 an annual fly monitoring in 16 fruits farms to understand populations dynamics ofD. suzukiiand to survey drosophilid communities.

RESULTS

We report here the first observation ofZaprionus tuberculatusMalloch, 1932 (Diptera: Drosophilidae) in mainland France. Over the whole monitoring, we trapped a total of 111 specimens in a fig orchard located in southern France (Salses-le-Château), both in fig trees and nearby hedgerows. The first detection ofZ. tuberculatusoccurred in July 2022 in the hedgerow and captures continued until January 2023 with an interruption in November and December. In addition, in this orchard we collected overripe figs in September 2023 from which over 15Z. tuberculatushave emerged in the following two weeks.

CONCLUSION

The pest status ofZ. tuberculatusand its potential risk for agriculture is not clear, but the pest behavior of the close-relative speciesZaprionus indianus, especially on figs, should be a warning point for the entry ofZ. tuberculatusinto the EU and France, as they may have similar nutritional ecology. The pest status, the establishment and the future spread ofZ. tuberculatusshould thus be monitored to assess possible damages to fruits productions.
AP-LASR: Automated Protein Libraries from Ancestral Sequence Reconstruction
Authors: VanAntwerp James , Mardikoraem Mehrsa , Pascual Nathaniel , Woldring Daniel
Published: October 2023

Background

Ancestral sequence reconstruction (ASR) provides an informative roadmap of evolutionary protein sequence space that benefits protein design and engineering in pursuitof high stability and diverse functionality. Using statistical and biological knowledge, ASR can determine the most probable ancestor among potential alternative amino acid states. However, the inherent uncertainty of ASR can be further leveraged to determine viable “nearby” ancestors with wide-ranging functionalities by sampling alternative amino acid states.

Results

Here we introduce AP-LASR which i) automates ASR and ii) leverages uncertainty in ASR to generate diverse protein sequence libraries that consist of ancestral sequences and near-ancestor sequences. In addition to automating pre-processing tasks (e.g., data cleaning, multiple sequence alignment, and software dependency management), AP-LASR offers several user-definable hyperparameters (e.g., input data size, ancestral probability cut-off, and sequence supplementation) to control the properties of the generated library. AP-LASR features an improved eLnP score (a metric for quantifying reconstructed ancestral sequence confidence) compared to FireProtASR, a well-established ASR workflow, for all four functionally diverse protein families studied. Furthermore, the rigorous statistical analysis undertaken in this study elucidates the influence of hyperparameters on ASR, enabling researchers to refine AP-LASR to their specific research.

Conclusion

AP-LASR offers an automated ASR experience that surpasses existing software by including a novel library design feature, powering curated protein libraries for wet-lab evaluation. We demonstrate how computational parameters impact the quality of ASR results, library composition, and the tradeoffs therein. AP-LASR offers a powerful tool for protein engineers to efficiently navigate the vast protein sequence landscape.

Software available at:https://github.com/WoldringLabMSU/AP-LASR
New realm of precision multiplexing enabled by massively-parallel single molecule UltraPCR
Authors: Lai Janice H. , Keum Jung won , Lee Haeun G. , Molaei Mehdi , Blair Emily J. , Li Sixing , Soliman Jesse W. , Raol Vedant K. , Barker Camille L. , Fodor Stephen P.A. , Fan H. Christina , Shum Eleen Y.
Published: October 2023

PCR has been a reliable and inexpensive method for nucleic acid detection in the past several decades. In particular, multiplex PCR is a powerful tool to analyze many biomarkers in the same reaction, thus maximizing detection sensitivity and reducing sample usage. However, balancing the amplification kinetics between amplicons and distinguishing them can be challenging, diminishing the broad adoption of high order multiplex PCR panels. Here, we present a new paradigm in PCR amplification and multiplexed detection using UltraPCR. UltraPCR utilizes a simple centrifugation workflow to split a PCR reaction into ∼34 million partitions, forming an optically clear pellet of spatially separated reaction compartments in a PCR tube. Afterin situthermocycling, light sheet scanning is used to produce a 3D reconstruction of the fluorescent positive compartments within the pellet. At typical sample DNA concentrations, the magnitude of partitions offered by UltraPCR dictate that the vast majority of target molecules occupy a compartment uniquely. This single molecule realm allows for isolated amplification events, thereby eliminating competition between different targets and generating unambiguous optical signals for detection. Using a 4-color optical setup, we demonstrate that we can incorporate 10 different fluorescent dyes in the same UltraPCR reaction. We further push multiplexing to an unprecedented level by combinatorial labeling with fluorescent dyes — referred to as “comboplex” technology. Using the same 4-color optical setup, we developed a 22-target comboplex panel that can detect all targets simultaneously at high precision. Collectively, UltraPCR has the potential to push PCR applications beyond what is currently available, enabling a new class of precision genomics assays.
Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum
Authors: Gonçalves Osiel S. , Fernandes Alexia S. , Tupy Sumaya M. , Ferreira Tauanne G. , Almeida Luciano N. , Creevey Christopher J. , Santana Mateus F.
Published: October 2023

The prevalence and abundance of Acidobacteriota raise concerns about their ecological function and metabolic activity in the environment. Studies have reported the potential of some members of Acidobacteriota to interact with plants and play a significant role in biogeochemical cycles. However, their role in this context has not been extensively studied. Here, we performed a comprehensive genomic analysis of 758 metagenome-assembled genomes (MAGs) and 121 RefSeq genomes of Acidobacteriota. Our analysis revealed a high frequency of plant growth-promoting traits (PGPTs) genes in theAcidobacteriaceae, Bryobacteraceae, Koribacteraceae, andPyrinomonadaceaefamilies. These PGPTs include genes involved in nitrogen fixation, phosphorus solubilization, exopolysaccharide production, siderophore production, and plant growth hormone production. Expression of such genes was found to be transcriptionally active in different environments. In addition, we identified numerous carbohydrate-active enzymes and peptidases involved in plant polymer degradation. By applying an in-depth insight into the diversity of the phylum, we expanded previous role in carbon, nitrogen, sulfur, and trace metal cycling. This study underscores the distinct potential ecological roles of each of these taxonomic groups, providing valuable insights for future research.
Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma
Authors: Petrucciani Alexa , Hoerter Alexis , Kotze Leigh , Du Plessis Nelita , Pienaar Elsje
Published: October 2023

Tuberculosis (TB) remains a global public health threat with increasing prevalence. Understanding the dynamics of host-pathogen interactions within TB granulomas will assist in identifying what leads to successful elimination of infection.In vitroTB models provide a controllable environment to study these granuloma dynamics. Previously we developed a biomimetic 3D spheroid granuloma model that controls bacteria better than a traditional monolayer culture counterpart. We used agent-based simulations to predict the mechanistic reason for this difference. Our calibrated simulations were able to predict heterogeneous bacterial dynamics that are consistent with experimental data. In one group of simulations, spheroids are found to have a higher macrophage activation than their traditional counterparts, leading to better bacterial control. This higher macrophage activation in the spheroids was not due to higher T cell activation, rather fewer activated T cells were able to activate more macrophages due to the proximity of these cells within the spheroid. In a second group of simulations, spheroids again have more macrophage activation but also more T cell activation, specifically CD8+ T cells. This higher level of CD8+ T cell activation is predicted to be due to the proximity of these cells to the cells that activate them. Multiple mechanisms of control were predicted. Virtual knockouts show one group has a CD4+ T cell dominant response, while the other has a mixed/CD8+ T cell dominant response. Lastly, we demonstrated that the initial structure and movement rules work synergistically to reduce bacterial load. These findings provide valuable insights into how the structural complexity ofin vitromodels impacts immune responses. Moreover, our study has implications for engineering more physiologically relevantin vitromodels and advancing our understanding of TB pathogenesis and potential therapeutic interventions.
Differences Between Brachial And Aortic Blood Pressure In Adolescence and their implications for diagnosis of hypertension
Authors: Hughes Alun D , Smith George Davey , Howe Laura D , Lawlor Deborah , Jones Siana , Park Chloe M , Chaturvedi Nish
Published: October 2023

Objectives

Blood pressure is the leading global cause of mortality, and its prevalence is increasing in children and adolescents. Aortic blood pressure (BP) is lower than brachial BP in adults. We aimed to assess the extent of this difference and its impact on the diagnosis of hypertension among adolescents.

Methods

We used data from 3850 participants from a UK cohort of births in the early 1990s in the Southwest of England, who attended their ∼17 year follow-up and had valid measures of brachial and aortic BP at that clinic (mean(SD) age 17.8(0.4)y, 66% female). Data are presented as mean differences [95% prediction intervals] for both sexes.

Results

Aortic systolic BP was lower than brachial systolic BP (male, -22.3[-31.2, - 13.3]mmHg; female, -17.8[-25.5, -10.0]mmHg). Differences between aortic and brachial diastolic BP were minimal. Based on brachial BP measurements, 101 males (6%) and 22 females (1%) were classified as hypertensive. In contrast, only nine males (<1%) and 14 females (<1%) met the criteria for hypertension based on aortic BP, and the predictive value of brachial BP for aortic hypertension was poor (positive predictive value = 13.8%). Participants with aortic hypertension had a higher left ventricular mass index than those with brachial hypertension.

Conclusions

Brachial BP substantially overestimates aortic BP in adolescents due to marked aortic-to-brachial pulse pressure amplification. The use of brachial BP measurement may result in an overdiagnosis of hypertension during screening in adolescence.
Predictive value of Serum CCL21 and CCL19 levels in heart failure patients : A prospective study
Authors: Zeng Wenfei , Li Ling , Wang Liman , Lin Biting , Lin Kailing , Yu Peng , Yu Huizhen
Published: October 2023

Background

Chemokine C-C motif ligand (CCL)21 and CCL19 are well-recognized to associate with adverse events of cardiovascular disease, especially long-term prognosis. However, few studies have reported its correlation with heart failure.

Purpose

To investigate and compare the predictive value of CCL21 and CCL19 serum levels in patients with heart failure.

Methods

In this prospective, observational, single-center study, 221 patients with heart failure and 55 healthy controls were included. ROC curves were generated to analyze and compare the serum levels of CCL21 and CCL19 in predicting all-cause mortality and composite events. Cox regression and Kaplan-Meier survival analyses were performed to identify independent risk factors for prognosis. Pearson correlation was used to measure the correlation between creatinine and CCL21 / CCL19 levels.

Results

The study observed 108 events (30 deaths and 78 occurred composite endpoints) over a median follow-up of 494.5(231.5,950.0) days. CCL21 showed strong predictive value for both all-cause mortality (AUC were 0.694,P=0.001) and composite endpoints (AUC 0.661,P=0.006 and <0.001). while the combination of CCL21 and NT-proBNP further improved the predictive power, with AUC being 0.796 and 0.662 on all-cause mortality and composite endpoints, respectively (bothP<0.001). K-M survival analysis revealed that patients with increased CCL21 and CCL19 exhibited higher all-cause mortality (bothP<0.05). Meanwhile, higher incidence of composite endpoint events was also observed in patients with elevated CCL21 (P<0.05). Importantly, multivariate COX regression analysis demonstrated that smoking, higher level of CCL21 and ischemic heart disease were independent risk factors for all-cause mortality (P<0.001). Furthermore, diabetes and elevation of CCL21 were associated with an increased risk of composite endpoints (P<0.001). On the other hand, changes in CCL19 levels showed a graded association with worse renal function, resulting in a slight increasing trend in G3 and G4/5, (HR = 2.64, 95% CI= 2.26-2.66, vs. HR 2.67, 95% CI 2.57-2.91, overall interactionP<0.05), with higher concentrations in G3 and G4/5(HR = 3.67, 95% CI= 3.27-3.85, vs. HR 4.11, 95% CI 3.67-4.38; overall interactionP<0.05).

Conclusions

Serum concentrations of CCL21 and CCL19 were significantly elevated in heart failure patients. High level of CCL21 is an independent risk factor for the adverse events in heart failure and may complement the prediction of those events which are less affected by renal function.
In vitrodevelopment and optimization of cell-laden injectable bioprinted gelatin methacryloyl (GelMA) microgels mineralized on the nanoscale
Authors: Sousa Mauricio Gonçalves da Costa , Balbinot Gabriela de Souza , Subbiah Ramesh , Visalakshan Rahul Madathiparambil , Tahayeri Anthony , Lima Verde Maria Elisa , Athirasala Avathamsa , Romanowicz Genevieve , Guldberg Robert E. , Bertassoni Luiz E.
Published: October 2023

Bone defects may occur in different sizes and shapes due to trauma, infections, and cancer resection. Autografts are still considered the primary treatment choice for bone regeneration. However, they are hard to source and often create donor-site morbidity. Injectable microgels have attracted much attention in tissue engineering and regenerative medicine due to their ability to replace inert implants with a minimally invasive delivery. Here, we developed novel cell-laden bioprinted gelatin methacrylate (GelMA) injectable microgels, with controllable shapes and sizes that can be controllably mineralized on the nanoscale, while stimulating the response of cells embedded within the matrix. The injectable microgels were mineralized using a calcium and phosphate-rich medium that resulted in nanoscale crystalline hydroxyapatite deposition and increased stiffness within the crosslinked matrix of bioprinted GelMA microparticles. Next, we studied the effect of mineralization in osteocytes, a key bone homeostasis regulator. Viability stains showed that osteocytes were maintained at 98% viability after mineralization with elevated expression of sclerostin in mineralized compared to non-mineralized microgels, indicating that mineralization effectively enhances osteocyte maturation. Based on our findings, bioprinted mineralized GelMA microgels appear to be an efficient material to approximate the bone microarchitecture and composition with desirable control of sample injectability and polymerization. These bone-like bioprinted mineralized biomaterials are exciting platforms for potential minimally invasive translational methods in bone regenerative therapies.
Overriding Mendelian inheritance inArabidopsiswith a CRISPR toxin-antidote gene drive that impairs pollen germination
Authors: Liu Yang , Jiao Bingke , Champer Jackson , Qian Wenfeng
Published: October 2023

Synthetic gene drives, inspired by natural selfish genetic elements, present transformative potential for disseminating traits that benefit humans throughout wild populations, irrespective of potential fitness costs. Here, we constructed a gene drive system called CRISPR-Assisted Inheritance utilizingNPG1(CAIN), which employs a toxin-antidote mechanism in the male germline to override Mendelian inheritance in plants. Specifically, a gRNA-Cas9 cassette targets the essentialNo Pollen Germination 1(NPG1) gene, serving as the toxin to block pollen germination. A recoded, CRISPR-resistant copy ofNPG1serves as the antidote, providing rescue only in pollen cells that carry the drive. To limit potential consequences of inadvertent release, we used self-pollinatingArabidopsis thalianaas a model. The drive demonstrated a robust 88–99% transmission rate over two successive generations, producing minimal resistance alleles that are unlikely to inhibit drive spread. Our study provides a strong basis for rapid genetic modification or suppression of outcrossing plant populations.
Unprecedented spike flexibility revealed by BSL3 Cryo-ET of active SARS-CoV-2 virions
Authors: Fukuhara Hideo , Dokainish Hisham M. , Kita Shunsuke , Tabata Koshiro , Takasu Akira , Huiskonen Juha T. , Anraku Yuki , Senda Toshiya , Stuart David I. , Sasaki Michihito , Orba Yasuko , Suzuki Yasuhiko , Sawa Hirofumi , Maenaka Katsumi
Published: October 2023

Understanding the molecular properties of SARS-CoV-2 is crucial to tackle future outbreaks. Current knowledge of the trimeric spike protein relies on truncated recombinant proteins and inactivated full-length forms, which may suffer from overstabilization. Here, we apply cryo-electron tomography (cryo-ET) at a Biosafety level 3 facility to study the virus structure in its native, active state. The virus particles show variable shapes with diffusible spikes, with the majority in typical prefusion conformations. Notably, we also identified unprecedented, atypical open-trimer prefusion states, revealing hidden flexibility. The sub-tomogram averaged structure suggests a loosely packed trimer. The observed dynamics uncover conserved cryptic regions that can be targeted for broadly effective vaccines. Structural analysis of active viruses will have implications on understanding overlooked fusion mechanism and vaccine, antibody/drug design. (124 words)

One-Sentence Summary

The BSL3 cryo-electron microscopy uncovered significant flexibility of the spike protein on active viruses, which will facilitate the design of broadly effective vaccines and drugs.
Seminal plasma inhibits Chlamydia trachomatis infectionin vitro, and may have consequences on mucosal immunity
Authors: Reot Louis , Adapen Cindy , Cannou Claude , Nunez Natalia , Lakoum Sabrine , Pimienta Camille , Lacroix Laetitia , Binois Olivier , Frydman Nelly , Nugeyre Marie-Thérèse , Le Grand Roger , Menu Elisabeth
Published: October 2023

Seminal plasma (SP) is the main vector ofC. trachomatis(CT) during heterosexual transmission from male to female. It has immunomodulatory properties and impacts the susceptibility to HIV-1 infection, but its role has not been explored during CT infection. In the female reproductive tract (FRT), CT infection induces cytokine production and neutrophil recruitment. The role of neutrophils during CT infection is partially described, they could be at the origin of the pathology observed during CT infection. During this study, we developed an experimentalin vitromodel to characterize the impact of CT infection and SP on endocervical epithelial cell immune response in the FRT. We also studied the impact of the epithelial cell response on neutrophil phenotype and functions. We showed that the production by epithelial cells of pro-inflammatory cytokines increased during CT infection. Moreover, the pool of SP as well as individuals SP inhibited CT infection in a dose-dependent manner. The pool of SP inhibited cytokine production in a dose-dependent manner. The pool of SP altered gene expression profiles of infected cells. The culture supernatants of cells infected or not with CT, in presence or not of the pool of SP, had an impact on neutrophil phenotype and functions: they affected markers of neutrophil maturation, activation and adhesion capacity, as well as the survival, ROS production and phagocytosis ability. This study proposes a novel approach to study the impact of the environment on the phenotype and functions of neutrophils in the FRT. It highlights the impact of the factors of the FRT environment, in particular SP and CT infection, on the mucosal inflammation and the need to take into account the SP component while studying sexually transmitted infections during heterosexual transmission from male to female.
TMEM65-dependent Ca2+extrusion safeguards mitochondrial homeostasis
Authors: Vetralla Massimo , Wischhof Lena , Cadenelli Vanessa , Scifo Enzo , Ehninger Dan , Rizzuto Rosario , Bano Daniele , De Stefani Diego
Published: October 2023

The bidirectional transport of Ca2+into and out of mitochondria is a conserved biological process controlling multiple events, including metabolism, signaling, and cell fate. In the presence of membrane potential driving mitochondrial Ca2+accumulation, transient changes of [Ca2+]mtin response to cytosolic [Ca2+] variations are ensured by a molecular machinery for Ca2+influx and efflux embedded in the inner mitochondrial membrane (IMM). While it is well established that influx relies on the Mitochondrial Calcium Uniporter (MCU), efflux was expected to be molecularly diversified, given the occurrence of functionally different exchange pathways with either Na+or H+1. Accordingly, dedicated transporters ensure proper Ca2+homeostasis and tightly regulated mitochondrial bioenergetics, but the process is not yet fully elucidated. We here demonstrate that TMEM65, a protein with an unknown biological function, is a fundamental component of the Ca2+efflux machinery of mitochondria. As the MCU, TMEM65 has a broad tissue expression and localizes to the IMM. Its overexpression dramatically enhances Na+- and Li+-dependent mitochondrial Ca2+extrusion, which is abrogated by the pharmacological inhibitor CGP-37157. Conversely, its downregulation chronically elevates resting mitochondrial Ca2+levels and inhibits efficient Ca2+efflux upon cellular activation, culminating in mitochondrial calcium overload and causing organelle dysfunction. Since TMEM65 has been associated with a severe human mitochondrial disease2, we deleted the TMEM65 homologues inCaenorhabditis elegans(CeTMEM65). While the two CeTMEM65 orthologs are dispensable for the survival at permissive growing conditions, their loss undermines embryonic developments when eggs are exposed to mild temperature-stress. In this regard, we find thatCeTMEM65 (null)alleles cause necrotic lesions that are suppressed by inhibiting the mitochondrial calcium uniporter MCU-1. Overall, these results unambiguously assign a primary role in mitochondrial Ca2+homeostasis to the orphan protein TMEM65. More importantly, our findings describe a novel molecular component that may be relevant in pathological settings in which excessive mitochondrial Ca2+accumulation critically contribute to degenerative pathways.
Oncogenic KEAP1 mutations activate TRAF2-NFκB signaling to prevent apoptosis in lung cancer cells
Authors: Deen Ashik Jawahar , Adinolfi Simone , Härkönen Jouni , Patinen Tommi , Liu Xiaonan , Laitinen Tuomo , Takabe Piia , Kainulainen Kirsi , Pasonen-Seppänen Sanna , Gawriyski Lisa M , Arasu Uma Thanigai , Selvarajan Ilakya , Mäkinen Petri , Laitinen Hanna , Kansanen Emilia , Kaikkonen Minna U , Poso Antti , Varjosalo Markku , Levonen Anna-Liisa
Published: October 2023

The Kelch-like ECH-associated protein 1 (KEAP1) – Nuclear factor erythroid 2-related factor 2 (NRF2) pathway is the major transcriptional stress response system in cells against oxidative and electrophilic stress. NRF2 is frequently constitutively active in many cancers, rendering the cells resistant to chemo- and radiotherapy. Loss-of-function (LOF) mutations in the repressor protein KEAP1 are common in non-small cell lung cancer, particularly adenocarcinoma. While the mutations can occur throughout the gene, they are enriched in certain areas, indicating that these may have unique functional importance. In this study, we show that in the GSEA analysis of TCGA lung adenocarcinoma RNA-seq data, the KEAP1 mutations in R320 and R470 were associated with enhanced Tumor Necrosis Factor alpha (TNFα)–Nuclear Factor kappa subunit B (NFκB) signaling as well as MYC and MTORC1 pathways. To address the functional role of these hotspot mutations, affinity purification and mass spectrometry (AP-MS) analysis of wild type (wt) KEAP1 and the mutants was employed to interrogate differences in the protein interactome. We identified TNF receptor associated factor 2 (TRAF2) as a putative protein interaction partner. Both mutant KEAP1 forms showed increased interaction with TRAF2 and other anti-apoptotic proteins, suggesting that apoptosis signalling could be affected by the protein interactions. A549 lung adenocarcinoma cells overexpressing mutant KEAP1 showed high TRAF2-mediated NFκB activity and increased protection against apoptosis, XIAP being one of the key proteins involved in anti-apoptotic signalling. To conclude, KEAP1 R320Q and R470C and its interaction with TRAF2 leads to activation of NFκB pathway, thereby protecting against apoptosis.
Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists
Authors: Lee Hower , Langseth Christoffer Mattsson , Salas Sergio Marco , Metousis Andreas , Alana Eneritz Rueda , Garcia-Moreno Fernando , Grillo Marco , Nilsson Mats
Published: October 2023

Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in-situ expression maps of hundreds of genes. We exploit direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-basedin situcombinatorial barcoding, to achieve high detection efficiency, high throughput and large multiplexing. We validate the method across a number of species, and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to highthroughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
Inferring ecological selection from multidimensional community trait distributions along environmental gradients
Authors: Kaarlejärvi Elina , Itter Malcolm , Tonteri Tiina , Hamberg Leena , Salemaa Maija , Merilä Päivi , Vanhatalo Jarno , Laine Anna-Liisa
Published: October 2023

Understanding the drivers of community assembly is critical for predicting the future of biodiversity and ecosystem services. While trait-based frameworks are often used to this end, correlations among traits and the assumption of unimodal trait-abundance distributions confound detection of the underlying processes. To overcome these caveats, here we quantify multidimensional trait distributions of communities (community trait niches), which we use to identify ecological selection types shaping communities along environmental gradients. We find that directional, stabilizing, and divergent selection all modify community trait niches in over 3600 boreal forest understory plant communities, and selection on a particular trait may change from one type to another over time. Our results provide novel and rare empirical evidence from a natural system for divergent selection. The results also show that while higher trait diversity (measured as trait niche volume) is generally associated with higher species richness, high resource availability may enable tighter niche packing. Jointly our approach provides a framework for identifying key traits under selection and facilitates the detection of processes underlying community dynamics.