bluuebunny/crossref_metadata_2025 huggingface dataset:
Limberg Flap for Lateral Midface Reconstruction
Authors: Gualtieri Matteo , Scivoletto Giulia , Pitino Francesca , D’Archivio Lanfranco , Valentini Valentino
Published: September 2024

Several local skin flaps and tissue rearrangement techniques have been described in the literature, including the rhomboid flap. The Limberg flap is one of the most versatile local flaps that can be used for reconstruction of a wide range of skin defects in different parts of the body. The purpose of this study is to demonstrate the safety and applicability of the Limberg flap for reconstruction of skin facial defects, particularly after cutaneous tumor resection.

The following article presents a retrospective case series of 8 patients in whom the Limberg flap was used to reconstruct skin defects resulting from malignant tumor resections in the lateral part of the face. No restrictions were collected regarding etiology, location, size, age, sex, or any other patient factors. The recruited patients were treated in the Maxillofacial Surgery Unit of Floraspe Renzetti Hospital of Lanciano and the study was conducted in collaboration with Sapienza University of Rome, from April 2023 to April 2024.

All the flaps settled with no complications and all the patients were FOD (free of disease) 6 months after surgery. So, in accordance with the literature, the Limberg flap turns out to be a rapid and reliable option that could be easily applied for small (size around 1–2 cm) and medium-sized (size around 2–4 cm) cutaneous defects of the face even for the oldest and/or emaciated patients.
Whole blood: Total blood product ratio impacts survival in injured children
Authors: Feeney Erin V. , Morgan Katrina M. , Spinella Philip C. , Gaines Barbara A. , Leeper Christine M.
Published: September 2024

BACKGROUND

Some studies in both children and adults have shown a mortality benefit for the use of low titer group O whole blood (LTOWB) compared with component therapy for traumatic resuscitation. Although LTOWB is not widely available at pediatric trauma centers, its use is increasing. We hypothesized that in children who received whole blood after injury, the proportion of whole blood in relation to the total blood product resuscitation volume would impact survival.

METHODS

The trauma database from a single academic pediatric Level I trauma center was queried for pediatric (age <18 years) recipients of LTOWB after injury (years 2015–2022). Weight-based blood product (LTOWB, red blood cells, plasma, and platelet) transfusion volumes during the first 24 hours of admission were recorded. The ratio of LTOWB to total transfusion volume was calculated. The primary outcome was in-hospital mortality. Multivariable logistic regression model adjusted for the following variables: age, sex, mechanism of injury, Injury Severity Score, shock index, and Glasgow Coma Scale score. Adjusted odds ratio representing the change in the odds of mortality by a 10% increase in the LTOWB/total transfusion volume ratio was reported.

RESULTS

There were 95 pediatric LTOWB recipients included in the analysis, with median (interquartile range [IQR]) age of 10 years (5–14 years), 58% male, median (IQR) Injury Severity Score of 26 (17–35), 25% penetrating mechanism. The median (IQR) volume of LTOWB transfused was 17 mL/kg (15–35 mL/kg). Low titer group O whole blood comprised a median (IQR) of 59% (33–100%) of the total blood product resuscitation. Among patients who received LTOWB, there was a 38% decrease in in-hospital mortality for each 10% increase in the proportion of WB within total transfusion volume (p < 0.001) after adjusting for age, sex, mechanism of injury, Injury Severity Score, shock index, and Glasgow Coma Scale score.

CONCLUSION

Increased proportions of LTOWB within the total blood product resuscitation was independently associated with survival in injured children. Based on existing data that suggests safety and improved outcomes with whole blood, consideration may be given to increasing the use of LTOWB over CT resuscitation in pediatric trauma resuscitation.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level III.
Neural Maturation Provides the Stability of Representation and the Solution for Understanding Complex Concepts
Authors: Watanabe Hiroyasu
Published: September 2024

summary

Recent advancements in realizing human-like brain functions through artificial intelligence have progressed significantly day by day. However, much of this astonishing progress in AI does not necessarily require an understanding of modern molecular biology. Here, I illustrate the significance of neural maturation in neural network-based information processing models. In both supervised and reinforcement learning paradigms, immature transmission can learn properties like normal high-fidelity conditions but lose these properties after reaching catastrophic points. I then investigated genes responsible for neuronal maturation and found that the candidate gene KCNH7 is expressed at higher levels during mouse brain development. In the simulated neural model with the KCNH7 channel property, the excitation threshold increased, resulting in a linear response property. These properties enhanced the stability of representation recall and enabled the comprehension of complex concepts in unsupervised learning models.

These results highlight the importance of neural maturation in achieving higher recognition abilities in adults.
Novel antibiotic resistance genes from the hospital effluent are disseminated into the marine environment in Norway
Authors: Radisic Vera , Victor Manish P. , Grevskott Didrik H. , Marathe Nachiket P.
Published: September 2024

Hospital effluent comprises feces of many individuals, including patients undergoing antibiotic treatment. Although, hospital effluent is an important source for contamination of the environment with antibiotic resistance genes (ARGs) and pathogens, how hospital effluent in a low resistance setting contributes to antimicrobial resistance (AMR) in the environment is largely understudied. The aim of our study was to understand the microbiota and resistome of hospital effluent, and its role in the spread of AMR in the marine environment in Norway. We further aimed at describing/characterizing novel resistance factors from hospital effluent and the receiving sewage treatment plant (STP). 24-hour composite samples of the hospital effluent and the influent and effluent of the receiving STP were collected at two sampling time-points (February and April 2023) in Bergen city, Norway. Isolation ofEscherichia coliandKlebsiellaspp. was performed, using ECC and SCAI plates with cefotaxime, tigecycline or meropenem, followed by antibiotic susceptibility testing, using EUVSEC3 plates. Whole-genome sequencing of selected strains (n=36) and shotgun metagenomics of sewage samples (n=6) were performed, using Illumina NovaSeq. ARGs were identified with USEARCH, and known and novel ARGs were assembled with fARGene. AllE. colistrains (n=66) were multidrug-resistant (MDR), while 92.3% of theKlebsiellaspp. strains (n=55) showed MDR phenotype. The sequenced strains carried multiple clinically important ARGs, including carbapenemases such as NDM-5 (n=3) and KPC-3 (n=3). We obtained 238 Gigabases of sequence data from which we identified 676 unique ARGs with >200 ARGs shared across samples. We assembled 1,205 ARGs using fARGene, 365 gene sequences represented novel ARGs (< 90% amino acid (aa) identity). Both known and novel ARGs (n=54) were shared between the hospital effluent and the treated effluent of the receiving STP. We show that hospital effluent in Norway has a high diversity of both known and novel ARGs. Our study demonstrates that hospital effluent is a source of clinically relevant pathogens, as well as known and novel ARGs, reaching the marine environment in Norway through treated sewage.
Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship
Authors: Carlisle David , Cunningham-Oakes Edward , Booth June , Frankland Andrew , McDowell Michael , Pilgrim Jack , Rzeszutek Aleksandra , Evans Ceri , Larkin Susan , Li Ang , Loftus Christopher , Samuel Merna , Scott Nicola , Swithenbank Luke , Owen Victoria , Darby Alistair C , Smielewska Anna
Published: September 2024

Background

Antimicrobial resistance (AMR) poses a significant global health challenge, resulting in over 1.27 million deaths in 2019 and projected to cause up to 10 million deaths annually in the future. To address this issue, the healthcare sector requires rapid and accurate bacterial identification, which is currently not readily available for effective antimicrobial stewardship. In a UK national first, we implemented 16S ribosomal RNA (rRNA) sequencing using Oxford Nanopore Technology (ONT) in an NHS setting to enhance diagnostic capabilities, aiming to reduce antibiotic misuse and improve patient outcomes.

Methods

We implemented 16S rRNA sequencing via ONT, running samples from seven NHS hospitals across Cheshire and Merseyside. We focused on samples from sterile sites, such as “pus”, “fluid”, and “tissue”, typically collected from critical care units. The assay was validated against traditional methods including Sanger sequencing and MALDI-TOF, with a turnaround time of 24-72 hours. Clinical impact was measured by analysing changes in antibiotic regimens and patient outcomes based on 16S assay results over a period of several months post-launch.

Findings

ONT 16S rRNA sequencing significantly impacted antibiotic treatment in 34.2% of cases, reducing patient stays and outperforming traditional methods by detecting additional bacterial organisms and identifying bacteria missed by reference labs. It provided species-level identification and confirmed non-infectious conditions in 5.4% of cases, aiding alternative treatment decisions. Its speed, cost-effectiveness, and minimal training requirements contributed to its successful integration into clinical practice.

Interpretation

The integration of ONT 16S sequencing into routine NHS diagnostics has significantly improved antimicrobial stewardship by offering a faster, more sensitive, and accurate bacterial identification method. Earlier use of this assay in cases where routine cultures are likely to fail could enhance patient outcomes further by enabling timely, targeted antibiotic therapies, reducing hospital stays, and curbing unnecessary antibiotic use.
Medication adherence and hospitalizations in older patients with coronary heart disease in Vietnam
Authors: Van Nguyen Tan , Hang Nguyen Thi Thuy , Dung Truong Ngoc , Viet Nguyen Quoc , Huy Nguyen Quang , Huy Nguyen Quoc , Trinh Ngo Thi Kim , Amsalu Erkihun , Wong Wei Jin , Nguyen Tu Ngoc
Published: September 2024

Aim

This study aimed to assess medication adherence among older people with coronary heart disease and its relationship with hospitalizations.

Methods

This is a prospective cohort study conducted at the outpatient clinics of a major hospital in Vietnam from November 2022 to June 2023. Consecutive older patients with coronary heart disease were recruited and followed for 6 months. Medication adherence was defined using the five[item Medication Adherence Report Scale (MARS-5). Multivariable logistic regression models were applied to examine the impact of medication adherence on hospitalization due to cardiovascular disease (CVD) and all-cause hospitalization.

Results

There were 643 participants. They had a mean age of 73 (SD 8), and 74.3% were male. Overall, 76.4% (491/643) were classified as “adherence”. Over 6 months follow-up, 23.3% of the participants admitted to hospital (9.2% were CVD-hospitalization). The CVD-hospitalization rate was significantly higher in the non-adherence group compared to the adherence group (13.8% versus 7.7%, p = 0.023, respectively). In logistic regression models, medication adherence was associated with a significant reduced odds of CVD hospitalization (adjusted OR 0.48, 95%CI 0.27 – 0.86). Medication adherence was also associated with a trend of reduced all-cause hospitalization (adjusted OR 0.75, 95%CI 0.49 – 1.15).

Conclusions

This study showed a positive relationship between medication adherence and reduced risk of CVD hospitalization in older people with coronary heart disease. Healthcare providers should consider incorporating adherence assessment into the long-term care for older patients with coronary heart disease.
Textual Triage: Assessing GPT4 for Classification of Free-Text Medication-Related Messages for Hypertension Management
Authors: Batugo Ashley , Hwang Sy , Davoudi Anahita , Luong Thaibinh , Lee Natalie , Mowery Danielle L
Published: September 2024

Patient-generated free-text messages are a well-recognized source of clinical burden and burnout for clinicians. Machine learning approaches such as Large Language Models (LLMs) may be applied to alleviate this burden by automatically triaging and classifying messages, but their performance in this domain has not been fully characterized. In this study, we analyzed the effectiveness of GPT4 for classifying patient and provider messages for hypertension management through prompt engineering, comparing its performance to an alternative unsupervised generative statistical approach. The results of this study suggest GPT is promising for classification of medical-related messages even with very few guiding examples.
Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations
Authors: Liu Jason , Borsari Beatrice , Li Yunyang , Liu Susanna , Gao Yuan , Xin Xin , Lou Shaoke , Jensen Matthew , Garrido-Martín Diego , Verplaetse Terril , Ash Garrett , Zhang Jing , Girgenti Matthew J. , Roberts Walter , Gerstein Mark
Published: September 2024

Psychiatric disorders are complex and influenced by both genetic and environmental factors. However, studying the full spectrum of these disorders is hindered by practical limitations on measuring human behavior. This highlights the need for novel technologies that can measure behavioral changes at an intermediate level between diagnosis and genotype. Wearable devices are a promising tool in precision medicine, since they can record physiological measurements over time in response to environmental stimuli and do so at low cost and minimal invasiveness. Here we analyzed wearable and genetic data from a cohort of the Adolescent Brain Cognitive Development study. We generated >250 wearable-derived features and used them as intermediate phenotypes in an interpretable AI modeling framework to assign risk scores and classify adolescents with psychiatric disorders. Our model identifies key physiological processes and leverages their temporal patterns to achieve a higher performance than has been previously possible. To investigate how these physiological processes relate to the underlying genetic architecture of psychiatric disorders, we also utilized these intermediate phenotypes in univariate and multivariate GWAS. We identified a total of 29 significant genetic loci and 52 psychiatric-associated genes, including ELFN1 and ADORA3. These results show that wearable-derived continuous features enable a more precise representation of psychiatric disorders and exhibit greater detection power compared to categorical diagnostic labels. In summary, we demonstrate how consumer wearable technology can facilitate dimensional approaches in precision psychiatry and uncover etiological linkages between behavior and genetics.
Evaluating the Joint Effects of Recurrent Copy Number Variants and Polygenic Scores on the Risk of Psychiatric Disorders in the iPSYCH2015 Case-Cohort Sample
Authors: Vaez Morteza , Montalbano Simone , Waples Ryan , Krebs Morten Dybdahl , Hellberg Kajsa-Lotta Georgii , Gådin Jesper , Bybjerg-Grauholm Jonas , Mortensen Preben B. , Børglum Anders D. , Nordentoft Merete , Geschwind Daniel H. , Helenius Dorte , Werge Thomas , Schork Andrew J. , Ingason Andrés
Published: September 2024

The impact of rare recurrent copy number variants (rCNVs) and polygenic background attributed to common variants, on the risk of psychiatric disorders is well-established in separate studies. However, it remains unclear how polygenic background modulates the effect of rCNVs. Using the population-representative iPSYCH2015 case-cohort sample (N=96,599), we investigated the association between absolute risk of psychiatric disorders and carriage of rCNVs and polygenic scores (PGS), as well as the interaction effect between the two on disease risk. Carriers of rCNVs with higher gene constraint scores had an increased absolute risk for autism, ADHD, and schizophrenia, but not depression, whereas an increase in PGS for each respective disorder was associated with higher absolute risk across all four disorders. Similarly, elevated absolute risks were observed with the increase of both PGS and gene constraints of rCNVs except in the case of depression. In contrast to some previous case-control studies, our joint analysis of rCNV groups and PGS revealed no indication of significant interactive effect between these two factors on disease risk. Also, we found no significant interactions of PGS with any of the most common individual rCNVs, except in the case of 16p13.11 duplication, which was found to attenuate the effect of ADHD-PGS on the absolute risk of ADHD. This study advances our understanding of the interplay between rare and common important genetic risk factors for major psychiatric disorders and sheds light on the importance of population-based samples in implementing precision medicine.
Vulnerable caribou and moose populations display contrasting responses to mountain pine beetle outbreaks and management.
Authors: Griffin Laura L , Finnegan Laura , Duval Julie , Ciuti Simone , Morera-Pujol Virginia , Li Haitao , Burton Cole
Published: September 2024

Rising global temperatures and changing landscape conditions have led to widespread mountain pine beetle (MPB) outbreaks in western North America. Extensive management has been implemented in response, via forest harvesting and prescribed burning. However, the impacts of MPB and MPB-management on ungulate populations, particularly caribou and moose, remain poorly studied. Given the differing specialisations of these species (caribou are habitat specialists, moose are generalists), their responses to these disturbances may vary. This could, in turn, lead to unintended, indirect effects (e.g., disturbance-mediated apparent competition, whereby increased moose presence results in increased predator presence, with resultant caribou declines). Unravelling these responses is crucial for informing MPB management and ensuring that applied actions do not exacerbate adverse effects. We assessed the effects of early-stage MPB-infestation, harvest, and fire, on habitat selection by caribou (boreal and central mountain designatable units) and moose in west-central Alberta. We built resource selection functions and functional response models using GPS collar data collected 3-5 years after MPB infestation and found that responses varied between species. Caribou had complex seasonal responses to MPB, generally avoiding areas with more MPB disturbance in winter but using them in summer. Caribou typically avoided harvested and burned areas, though this was dependent on the overall degree of disturbance within their ranges. In contrast, moose had positive responses to both MPB and burned areas year-round. These findings suggest that MPB may negatively impact long-term winter habitat availability for threatened caribou populations, but may have positive impacts on moose habitat. However, moose use of MPB-impacted areas could further affect caribou by contributing to disturbance-mediated apparent competition. Synthesis and applications: The negative impacts of forest harvest and burning on caribou suggests that less intensive actions are required for MPB management within caribou ranges. While moose selectively used harvested and burned areas, it is possible that they may have adverse responses to cumulative disturbance over time. As caribou and moose responded to MPB soon after infestation, ongoing monitoring is required to detect MPB early and facilitate proactive management, though further study is needed to determine the most effective actions.
A yeast-based reverse genetics system to generate HCoV-OC43 reporter viruses encoding an eighth sgRNA
Authors: Duguay Brett A. , Tooley Trinity H. , Pringle Eric S. , Rohde John R. , McCormick Craig
Published: September 2024

Coronaviruses have large, positive-sense single-stranded RNA genomes that challenge conventional strategies for mutagenesis. Here, we report the development of a new reverse genetics system for the endemic human coronavirus (HCoV) OC43 that utilizes transformation-associated recombination (TAR) to assemble complete viral genomes from dsDNA genome fragments via homologous recombination inSaccharomyces cerevisiae. Following cDNA synthesis from HCoV-OC43 viral RNA, we used TAR to capture fragments of the HCoV-OC43 genome to store as sequence-validated dsDNA parts. We performed combinatorial assembly in yeast to obtain an intact dsDNA copy of the HCoV-OC43 genome sufficient to launch viral replication upon introduction into human cells, yielding the yeast assembled OC43YAvirus. We also expanded the OC43YAgenome by inserting an eighth body transcription regulatory sequence (B-TRS) and an mClover3-H2B reporter gene between theMandNgenes, designed to allow the reporter protein to be translated from its own subgenomic mRNA. We thoroughly evaluated OC43YAand the OC43-mCloYAreporter virus, and demonstrated comparable viral gene expression, fitness in cell culture, and susceptibility to antivirals, compared to their natural progenitor. In summary, this new HCoV-OC43 reverse genetics system provides a modular platform for mutagenesis and combinatorial assembly of HCoV-OC43 genomes, and demonstrates the feasibility of expanding the genome while avoiding disruption of native coding sequences.

IMPORTANCE

Human coronavirus OC43 (HCoV-OC43) is an endemic human coronavirus that typically causes relatively mild respiratory illnesses and displays seasonal patterns of infection. We developed a new system to assemble DNA copies of HCoV-OC43 genomes and generate recombinant viruses for research purposes. This system uses yeast, first to capture segments of DNA encompassing the entire RNA-based viral genome, and then to stitch them together into complete DNA genome copies that can be amplified in bacteria and introduced into human cells to initiate an infectious cycle, ultimately yielding recombinant viruses with comparable properties to their natural progenitors. We also devised a strategy to expand the viral genome, adding a gene for a reporter protein encoded by an additional eighth subgenomic mRNA. This yeast-based genome assembly system provides a modular platform for rapid mutagenesis and combinatorial assembly of HCoV-OC43 genomes and demonstrates the feasibility of expanding the genome.
Histone demethylase enzymes KDM5A and KDM5B modulate immune response by suppressing transcription of endogenous retroviral elements
Authors: Chen Huadong , Sarah Letitia , Pucciarelli Daniela , Mao Ying , Diolaiti Morgan E. , Galonić Fujimori Danica , Ashworth Alan
Published: September 2024

Epigenetic factors, including lysine-specific demethylases such as the KDM5 paralogs KDM5A and KDM5B have been implicated in cancer and the regulation of immune responses. Here, we performed a comprehensive multiomic study in cells lacking KDM5A or KDM5B to map changes in transcriptional regulation and chromatin organization. RNA-seq analysis revealed a significant decrease in the expression of Krüppel-associated box containing zinc finger (KRAB-ZNF) genes in KDM5A or KDM5B knockout cell lines, which was accompanied by changes ATAC-seq and H3K4me3 ChIP-seq. Pharmacological inhibition of KDM5A and KDM5B catalytic activity with a pan-KDM5 inhibitor, CPI-455, did not significantly change KRAB-ZNF expression, raising the possibility that regulation of KRAB-ZNF expression does not require KDM5A and KDM5B demethylase activity. KRAB-ZNF are recognized suppressors of the transcription of endogenous retroviruses (ERVs) and HAP1 cells withKDM5AorKDM5Bgene inactivation showed elevated ERV expression, increased dsRNA levels and elevated levels of immune response genes. Acute degradation of KDM5A using a dTAG system in HAP1 cells led to increased ERV expression, demonstrating that de-repression of ERV genes occurs rapidly after loss of KDM5A. Co-immunoprecipitation of KDM5A revealed an interaction with the Nucleosome Remodeling and Deacetylase (NuRD) complex suggesting that KDM5A and NuRD may act together to regulate the expression of ERVs through KRAB-ZNFs. These findings reveal roles of KDM5A and KDM5B in modulating ERV expression and underscore the therapeutic potential of using degraders of KDM5A and KDM5B to modulate tumor immune responses.

Author Summary

The histone demethylases KDM5A and KDM5B are transcriptional repressors that play an important role in cancer and immune response, making them attractive drug targets. Unfortunately, small molecule inhibitors, including CPI-455, that block KDM5A and KDM5B enzymatic activity, have shown only limited effectiveness at suppressing cancer cell viability as single agents in vitro. In this study we undertook a multi-omics approach to map transcriptional and chromatin changes in KDM5A and KDM5B deficient cells compared to those treated with CPI-455. The datasets revealed that KDM5A and KDM5B modulate the expression of KRAB-ZNF genes and that loss of either gene was associated with increased expression of ERV genes and upregulation of immune response markers. Surprisingly, pharmacological inhibition of these enzymes did not phenocopy genetic ablation. In contrast, acute degradation of KDM5A using a dTAG system caused an increase in ERV expression, providing evidence that this immune modulation is independent of demethylase activity. Together with the limited success of small molecule inhibitors, our data provide strong rationale for the development of KDM5A and KDM5B degraders to modulate tumor immune responses.
Structural insights into the molecular recognition of integrin αVβ3 by RGD-containing ligands: The role of the specificity-determining loop (SDL)
Authors: Mariasoosai Charles , Bose Santanu , Natesan Senthil
Published: September 2024

Integrin αVβ3 is a prominent member of the “RGD-recognizing” integrin family of cell surface receptors. αVβ3 binds to various extracellular matrix (ECM) proteins and oxysterols such as 25-hydroxycholesterol, is implicated in several diseases, including cancer metastasis, lung fibrosis, inflammation, and autoimmune diseases, and is pursued as a valuable therapeutic target. Despite enormous efforts to seek a pure antagonist, to date, no single drug candidate has successfully reached clinics due to associated partial agonism and toxicity issues. Developing effective and safe inhibitors require a thorough understanding of the molecular interactions and structural changes related to the receptor’s activation and inhibition mechanisms. This study offers a comprehensive residue-residue contact and network analyses of the ligand-binding β-propeller βI domains (headpiece) based on all available experimental structures of integrin αVβ3 in unliganded, agonist-, antagonist-, and antibody-bound states. The analyses reveal many critical interactions that were not reported before and show that specific orientation and interactions of residues from the specificity-determining loop (SDL) are critical in molecular recognition and regulation. Also, the network analysis reveals that residues from the nearby allosteric site (site II) connect to the primary RGD-binding site via SDL, which likely acts as an interface between the two sites. Our results provide valuable insights into molecular interactions, structural changes, distinct features of the active and inactive headpiece conformations, the role of SDL in ligand recognition, and SDL-mediated allostery. Thus, the insights from this study may facilitate the designing of pure antagonists or site II-mediated allosteric modulators to integrin αVβ3 to treat various diseases.
Inducible and reversible SOD2 knockdown in mouse skeletal muscle drives impaired pyruvate oxidation and reduced metabolic flexibility
Authors: Ostrom Ethan L. , Stuppard Rudy , Mattson-Hughes Aurora , Marcinek David J.
Published: September 2024

Abstract Figure

Graphical Abstract

Highlights

SOD2 knockdown and recovery is achieved in skeletal muscle by using a shRNA targeted to SOD2 mRNA controlled by a tetracycline Response Element and reverse tetracycline transactivator protein

SOD2 KD is induced by administering doxycycline in the drinking water

Mitochondrial functional decline and recovery follows the time course of SOD2 protein decline and recovery

Sustained SOD2 KD precipitates reduced metabolic flexibility in skeletal muscle mitochondria characterized by impaired pyruvate respiration in the presence of other substrates

Introduction

Skeletal muscle mitochondrial dysfunction is a key characteristic of aging muscle and contributes to age related diseases such as sarcopenia, frailty, and type 2 diabetes. Mitochondrial oxidative distress has been implicated as a driving factor in these age-related diseases, however whether it is a cause, or a consequence of mitochondrial dysfunction remains to be determined. The development of more flexible genetic models is an important tool to test the mechanistic role of mitochondrial oxidative stress on skeletal muscle metabolic dysfunction. We characterize a new model of inducible and reversible mitochondrial redox stress using a tetracycline controlled skeletal muscle specific short hairpin RNA targeted to superoxide dismutase 2 (iSOD2).

Methods

iSOD2 KD and control (CON) animals were administered doxycycline for 3-or 12-weeks and followed for up to 24 weeks and mitochondrial respiration and muscle contraction were measured to define the time course of SOD2 KD and muscle functional changes and recovery.

Results

Maximum knockdown of SOD2 protein occurred by 6 weeks and recovered by 24 weeks after DOX treatment. Mitochondrial aconitase activity and maximum mitochondrial respiration declined in KD muscle by 12 weeks and recovered by 24 weeks. There were minimal changes in gene expression between KD and CON muscle. Twelve-week KD showed a small, but significant decrease in muscle fatigue resistance. The primary phenotype was reduced metabolic flexibility characterized by impaired pyruvate driven respiration when other substrates are present. The pyruvate dehydrogenase kinase inhibitor dichloroacetate partially restored pyruvate driven respiration, while the thiol reductant DTT did not.

Conclusion

We use a model of inducible and reversible skeletal muscle SOD2 knockdown to demonstrate that elevated matrix superoxide reversibly impairs mitochondrial substrate flexibility characterized by impaired pyruvate oxidation. Despite the bioenergetic effect, the limited change in gene expression suggests that the elevated redox stress in this model is confined to the mitochondrial matrix.
Criterion for assessing accumulated neurotoxicity of alpha-synuclein oligomers in Parkinson’s disease
Authors: Kuznetsov Andrey V.
Published: September 2024

The paper introduces a parameter called “accumulated neurotoxicity” of α-syn oligomers, which measures the cumulative damage these toxic species inflict on neurons over time, given the years it typically takes for such damage to manifest. A threshold value for accumulated neurotoxicity is estimated, beyond which neuron death is likely. Numerical results suggest that rapid deposition of α-syn oligomers into fibrils minimizes toxicity, indicating that the formation of Lewy bodies might play a neuroprotective role. Strategies such as reducing α-syn monomer production or enhancing degradation can decrease accumulated toxicity. In contrast, slower degradation (reflected by longer half-lives of monomers and free aggregates) increases toxicity, supporting the idea that impaired protein degradation may contribute to Parkinson’s disease progression. The study also examines the sensitivity of accumulated toxicity to different model parameters.
Fine-tuning sequence-to-expression models on personal genome and transcriptome data
Authors: Rastogi Ruchir , Reddy Aniketh Janardhan , Chung Ryan , Ioannidis Nilah M.
Published: September 2024

Genomic sequence-to-expression deep learning models, which are trained to predict gene expression and other molecular phenotypes across the reference genome, have recently been shown to have poor out-of-the-box performance in predicting gene expression variation across individuals based on their personal genome sequences. Here we explore whether additional training (fine-tuning) on paired personal genome and transcriptome data improves the performance of such sequence-to-expression models. Using Enformer as a representative pre-trained model, we explore various fine-tuning strategies. Our results show that fine-tuning improves cross-individual prediction performance over the baseline Enformer model for held-out individuals on genes seen during fine-tuning, with comparable performance to variant-based linear models commonly used in transcriptome-wide association studies. However, fine-tuning does not improve model generalizability on held-out genes, which contain sequences and variants unseen during fine-tuning, highlighting a remaining open challenge in the field.
Predicting bacterial fitness in Mycobacterium tuberculosis with transcriptional regulatory network-informed interpretable machine learning
Authors: Bustad Ethan , Petry Edson , Gu Oliver , Griebel Braden T. , Rustad Tige R. , Sherman David R. , Yang Jason H. , Ma Shuyi
Published: September 2024

Mycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis disease, the greatest source of global mortality by a bacterial pathogen. Mtb adapts and responds to diverse stresses such as antibiotics by inducing transcriptional stress-response regulatory programs. Understanding how and when these mycobacterial regulatory programs are activated could enable novel treatment strategies for potentiating the efficacy of new and existing drugs. Here we sought to define and analyze Mtb regulatory programs that modulate bacterial fitness. We assembled a large Mtb RNA expression compendium and applied these to infer a comprehensive Mtb transcriptional regulatory network and compute condition-specific transcription factor activity profiles. We utilized transcriptomic and functional genomics data to train an interpretable machine learning model that can predict Mtb fitness from transcription factor activity profiles. We demonstrated that this transcription factor activity-based model can successfully predict Mtb growth arrest and growth resumption under hypoxia and reaeration using only RNA-seq expression data as a starting point. These integrative network modeling and machine learning analyses thus enable the prediction of mycobacterial fitness under different environmental and genetic contexts. We envision these models can potentially inform the future design of prognostic assays and therapeutic intervention that can cripple Mtb growth and survival to cure tuberculosis disease.
Effects of residue substitutions on the cellular abundance of proteins
Authors: Schulze Thea K. , Lindorff-Larsen Kresten
Published: September 2024

Multiplexed assays of variant effects (MAVEs) make it possible to measure the functional impact of all possible single amino acid residue substitutions in a protein in a single experiment. Combination of variant effect data from several such experiments provides the opportunity to conduct large-scale analyses of variant effect scores measured across proteins, but can be complicated by variations in the phenotypes that are probed across experiments. Thus, using variant effect datasets obtained with similar MAVE techniques can help reveal general rules governing the effects of amino acid variation for a single molecular phenotype. In this work, we accordingly combined data from six individual variant abundance by massively parallel sequencing (VAMP-seq) experiments and analysed a total of 31,614 variant effect scores reporting solely on the impact of single amino acid residue substitutions on the cellular abundance of proteins. Using our combined variant effect dataset, we derived and analysed a collection of amino acid substitution matrices describing the average impact on cellular abundance of all residue substitution types in different structural environments. We found that the substitution matrices predict the cellular abundance of protein variants with surprisingly high accuracy when given structural information only in the form of whether a residue is buried or exposed. We thus propose our substitution matrix-based predictions as strong baselines for future abundance model development.
Gut-derived PPAR-γ signaling and risk of bacterial enteric infection: insight from thiazolidinedione users in a US population-based study
Authors: Birabaharan Morgan , Kaelber David C , Nizet Victor , Zarrinpar Amir
Published: September 2024

Background and Aims

The ongoing antimicrobial resistant crisis heralds the need for new therapeutics against enteric infection. In mouse models, colon epithelial peroxisome proliferator-activated receptor-γ (PPAR-γ) signaling limits oxygen and nitrate luminal bioavailability, thereby preventing bacterial pathogen colonization. However, whether this mechanism operates similarly in humans remains uncertain.

Methods

To investigate, we used the cloud-based TriNetX Analytics Platform which aggregates health records from 117 million patients across 66 US healthcare organizations, to assess the risk of bacterial enteric infection among diabetic patients prescribed thiazolidinediones, a class of PPAR-γ agonists, to other anti-diabetes medications.

Results

Among 85,117 thiazolidinedione users, we observed a 22-49% lower risk of bacterial enteric infections compared to users of other anti-diabetes medications. This reduction in risk was consistent across high-risk individuals, regardless of sex or age. Similar results were replicated in high-risk patients when thiazolidinedione users were directly compared to those on DPP-4 inhibitors.

Conclusion

These findings support the potential protective role of PPAR-γ signaling against bacterial enteric infection and call for further clinical investigation.
Diagnostic Performance of Systemic-Immune Inflammation Index for Overall and Complicated Acute Appendicitis: A Systematic Review and a Diagnostic Test Accuracy Meta-Analysis
Authors: Montero Javier Arredondo , Delgado-Miguel Carlos , Riveros Blanca Paola Pérez , Fernández-Atuan Rafael , Rico-Jiménez María
Published: September 2024

Background

This study aimed to analyze the systemic-immune inflammation index (SII)’s diagnostic performance in diagnosing acute appendicitis (AA) and discriminating between complicated acute appendicitis (CAA) and non-complicated acute appendicitis (NCAA).

Methods

This review was registered in PROSPERO (CRD42024587430). We included prospective or retrospective original clinical studies evaluating the diagnostic performance of SII in AA. A search was conducted in PubMed, Web of Science, Scopus, and OVID. Search terms and keywords were: (appendicitis OR appendectomy) AND (systemic-immune inflammation index OR SII). Two independent reviewers selected the articles and extracted relevant data. Methodological quality was assessed using the QUADAS2 index. A synthesis of the results, standardization of the metrics, four random-effect meta-analyses, and two Diagnostic Test Accuracy (DTA) meta-analyses were performed.

Results

Thirteen studies with data from 9083 participants, including 5255 patients with a confirmed diagnosis of AA and 3828 controls (CG), were included in this review. The random-effect meta-analysis of SII (AA vs. CG) included ten articles (3733 AA and 3510 controls) and resulted in a significant mean difference [95% CI] of 1072.46 [750.55,1394.37] (p<0.001). The random-effect meta-analysis of SII (CAA vs. NCAA) included nine articles (1116 CAA and 2984 NCAA) and resulted in a significant mean difference [95% CI] of 1294.2 [731.54,1856.86] (p<0.001). Subgroup meta-analysis for studies conducted in pediatric-only populations maintained statistical significance. The DTA meta-analysis (AA vs. CG) yielded a pooled sensitivity and specificity [95% CI] of 81.8 [75.2,86.9] % and 79.9 [68.2,88.1] %. The DTA meta-analysis (NCAA vs. CAA) resulted in a pooled sensitivity and specificity [95% CI] of 72.5 [49.6,87.6] % and 82.5 [65.1,92.2] %.

Conclusions

SII emerges as a robust tool for diagnosing AA and differentiating between NCAA and CAA. The retrospective nature of most of the included studies and their limited geographical distribution warrant further prospective multicenter studies to validate these findings.

Funding

None

Registration

PROSPERO (CRD42024587430).
Behavioural changes in frontotemporal dementia and their cognitive and neuroanatomical correlates
Authors: Rouse Matthew A. , Husain Masud , Garrard Peter , Patterson Karalyn , Rowe James B. , Lambon Ralph Matthew A.
Published: September 2024

Behavioural changes are a central feature of frontotemporal dementia (FTD); they occur in both behavioural-variant (bvFTD) and semantic dementia (SD)/semantic-variant primary progressive aphasia subtypes. In this study, we addressed two current clinical knowledge gaps; (i) are there qualitative or clear distinctions between behavioural profiles in bvFTD and SD, and (ii) what are the precise roles of the prefrontal cortex and anterior temporal lobes in supporting social behaviour? Resolving these conundrums is crucial for improving diagnostic accuracy and for the development of targeted interventions to treat challenging behaviours in FTD. Informant questionnaires to assess behavioural changes included the Cambridge Behavioural Inventory-Revised and two targeted measures of apathy and impulsivity. Participants completed a detailed neuropsychological battery to permit investigation of the relationship between cognitive status (including social-semantic knowledge, general semantic knowledge and executive function) with behaviour change in FTD. To explore changes in regional grey matter volume, a subset of patients had structural MRI. Diagnosis-based group comparisons were supplemented by a transdiagnostic approach which encompassed the spectrum of bvFTD, SD and “mixed” or intermediate cases. Such an approach is sensitive to the systematic graded variation in FTD and allows the neurobiological underpinnings of behaviour change to be explored across an FTD spectrum. We found a wide range of behavioural changes across FTD. Althoughquantitativelymore severe on average in bvFTD, as expected, the item-level analyses found no evidence forqualitativedifferences in behavioural profiles or “behavioural double dissociations” between bvFTD and SD. Comparisons of self and informant ratings revealed strong discrepancies in the perspective of the caregiver versus patient. Logistic regression revealed that neuropsychological measures had better discriminative accuracy for bvFTD versus SD than caregiver-reported behavioural measures. A principal component analysis of all informant questionnaire domains extracted three components, interpreted as reflecting: (1) apathy, (2) challenging behaviours and (3) activities of daily living. More severe apathy in both FTD subtypes was associated with (a) increased levels of impaired executive function and (b) anterior cingulate cortex atrophy. Questionnaire ratings of impaired behaviour did not correlate with either anterior temporal lobe atrophy or degraded social-semantic knowledge. Together, these findings highlight the presence of a wide range of behavioural changes in both bvFTD and SD, which vary by degree rather than quality. We recommend a transdiagnostic approach for future studies of the neuropsychological and neuroanatomical underpinnings of behavioural deficits in FTD.
External validation of prognostic and predictive gene signatures in head and neck cancer patients
Authors: Fossen Erlend I. F. , Moreira-Soares Mauricio , LeBlanc Marissa , Frigessi Arnoldo , Hovig Eivind , Lopez-Perez Laura , Estévez-Priego Estefanía , Hernandez Liss , Cabrera-Umpierrez Maria Fernanda , Fico Giuseppe , Tinhofer Ingeborg , Sachse Vanessa , Scheckenbach Kathrin , Le Tourneau Christophe , Kamal Maud , Thomas Steve , Pring Miranda , Licitra Lisa , De Cecco Loris , Cavalieri Stefano
Published: September 2024

Head and neck squamous cell carcinomas (HNSCC) are aggressive and heterogenous tumors with a high fatality rate. Many gene signatures (GS) have been developed with both prognostic and predictive significance. We aimed to externally validate five published GS in a large European collection of HNSCC patients. Gene expression from 1097 treatment-naïve HNSCC patients’ primary tumors was used to calculate scores for the five GS. Cox proportional hazard models were used to test the association between both 2-year overall survival and 2-year disease-free survival and the signature scores. The predictive role of GS was validated by comparing survival associations in patients receiving specific treatment (i.e., radiotherapy, systemic treatment) versus those who did not. We successfully externally validated all 5 GS, including two prognostic signatures, one signature as prognostic and predictive of sensitivity to systemic treatment, while signatures for cisplatin-sensitivity and radiosensitivity were validated as prognostic only.
Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells
Authors: Wellington Rachel , Cheng Xiaoyi , Campbell Clyde A. , Trapnell Cole , Espin-Palazon Raquel , Hadland Brandon , Doulatov Sergei
Published: September 2024

Hematopoietic stem cells (HSCs) arise in embryogenesis from a specialized hemogenic endothelium (HE). In this process, HE cells undergo a unique fate change termed endothelial-to-hematopoietic transition, or EHT. While induced pluripotent stem cells (iPSCs) give rise to HE with robust hemogenic potential, the generation of bona fide HSCs from iPSCs remains a challenge. Here, we map single cell dynamics of EHT during embryoid body differentiation from iPSCs and integrate it with human embryo datasets to identify key transcriptional differences betweenin vitroandin vivocell states. We further map ligand-receptor interactions associated with differential expression of developmental programs in the iPSC system. We found that the expression of endothelial genes was incompletely repressed during iPSC EHT. Elevated FGF signaling by FGF23, an endothelial pathway ligand, was associated with differential gene expression betweenin vitroandin vivoEHT. Chemical inhibition of FGF signaling during EHT increased HSPC generation in the zebrafish, while an FGF agonist had the opposite effect. Consistently, chemical inhibition of FGF signaling increased hematopoietic output from iPSCs. In summary, we map the dynamics of EHT from iPSCs at single cell resolution and identify ligand-receptor interactions that can be modulated to improve iPSC differentiation protocols. We show, as proof of principle, that chemical inhibition of FGF signaling during EHT improves hematopoietic output in zebrafish and the iPSC system.