bluuebunny/crossref_metadata_2025_split huggingface dataset:
FLIMPA: A versatile software for Fluorescence Lifetime Imaging Microscopy Phasor Analysis
Authors: Kapsiani Sofia , Läubli Nino F. , Ward Edward N. , Shehata Mona , Kaminski Clemens F. , Kaminski Schierle Gabriele S. 
Published: September 2024

AbstractFluorescence lifetime imaging microscopy (FLIM) is an advanced microscopy technique capable of providing a deeper understanding of the molecular environment of a fluorophore. While FLIM data were traditionally analysed through the exponential fitting of the fluorophores’ emission decays, the use of phasor plots is increasingly becoming the preferred standard. This is due to their ability to visualise the distribution of fluorescent lifetimes within a sample, offering insights into molecular interactions in the sample without the need for model assumptions regarding the exponential decay behaviour of the fluorophores. However, so far most researchers have had to rely on commercial phasor plot software packages, which are closed-source and rely on proprietary data formats. In this paper, we introduce FLIMPA, an opensource, stand-alone software for phasor plot analysis that provides many of the features found in commercial software, and more. FLIMPA is fully developed in Python and offers advanced tools for data analysis and visualisation. It enhances FLIM data comparison by integrating phasor points from multiple trials and experimental conditions into a single plot, while also providing the possibility to explore detailed, localised insights within individual samples. We apply FLIMPA to introduce a cell-based assay for the quantification of microtubule depolymerisation, measured through fluorescence lifetime changes of SiR-tubulin, in response to various concentrations of Nocodazole, a microtubule depolymerising drug relevant to anti-cancer treatment.
IL-27 neutralization to modulate the tumor microenvironment and increase immune checkpoint immunotherapy efficacy
Authors: Papargyris Loukas , Glaziou Quentin , Basset Laetitia , d’Almeida Sènan , Pignon Pascale , Jabrane-Ferrat Nabila , Blanquart Christophe , Delneste Yves , Tabiasco Julie 
Published: September 2024

AbstractTumor-associated macrophages (TAMs) accumulate in the majority of solid tumors, producing inflammatory cytokines and growth factors involved in tumor maintenance. They have recently emerged as targets for restoring an effective antitumor response and limiting tumor growth. In the present study, we investigated the potential of IL-27 neutralization to modify macrophage polarization and thus the tumor immune microenvironment.We monitored the effect of IL-27 neutralization on human macrophages and in vivo in a murine colon adenocarcinoma model.In this study, we demonstrated the importance of IL-27 in the generation of human immunoregulatory macrophages. Mechanistically, IL-27 neutralization reduced the immunosuppressive properties of macrophages. These modifications led to a reduction in the ability of macrophages to inhibit the function of CD4+and CD8+T cells. Furthermore, in vivo neutralization of IL-27 reduced MC38 tumor growth. Collectively, we uncovered the role of IL-27 in the immunosuppressive tumor microenvironment. IL-27 neutralization thus appears as a promising strategy to target macrophages in immunosuppressive TME and improve the clinical efficacy of immunotherapy protocols.
Validation of a refined protocol for mouse oral glucose tolerance testing without gavage
Authors: Pye Katherine R. , Lantier Louise , Ayala Julio E. , Beall Craig , Ellacott Kate L.J. 
Published: September 2024

AbstractA glucose tolerance test (GTT) is routinely used to assess glucose homeostasis in clinical settings and in preclinical research studies using rodent models. The procedure assesses the ability of the body to clear glucose from the blood in a defined time after a bolus dose. In the human clinical setting, glucose is ingested via voluntary consumption of a glucose-sweetened drink. Typically, in the rodent GTT oral gavage (gavage-oGTT) or (more commonly) intraperitoneal injection (IPGTT) are used to administer the glucose bolus. Although used less frequently, likely due to investigator technical and experience barriers, the former is the more physiologically relevant as it integrates the gastrointestinal tract (GI), including release of key incretin hormones. However, orally gavaging glucose in the GTT is also not without its limitations: gavaging glucose straight into the stomach bypasses potentially critical early glucose-sensing via the mouth (cephalic phase) and associated physiological responses. Furthermore, gavaging is stressful on mice, and this by itself can increase blood glucose levels. We have developed and validated a refined protocol for mouse oral GTT which uses a voluntary oral glucose dosing method, micropipette-guided drug administration (MDA), without the need for water deprivation. This approach is simple and non-invasive. It is less stressful for the mice, as evidenced by lower circulating corticosterone levels 10 minutes after glucose-dosing compared to oral gavage. This is significant for animal and investigator welfare, and importantly minimising the confounding effect of stress on mouse glucose homeostasis. Using a randomised cross-over design, we have validated the MDA approach in the oGTT against oral gavage in male and female C57BL/6J and C57BL/6N mice. We show the ability of this method to detect changes in glucose tolerance in diet-induced obese animals. Compared to oral gavage there was lower inter-animal variation in the MDA-oGTT. In addition to being more representative of the human procedure, the MDA-oGTT is easy and has lower barriers to adoption than the gavage oGTT as it is non-invasive and requires no specialist equipment or operator training. The MDA-oGTT a more clinically representative, accessible, and refined replacement for the gavage-oGTT for mouse metabolic phenotyping, which is simple yet overcomes significant deficiencies in the current standard experimental approaches.
Pharmacological Inhibition of Epac1 Protects against Pulmonary Fibrosis by Blocking FoxO3a Neddylation
Authors: Jankowski Katherine , Lemay Sarah E , Lozano-ojalvo Daniel , Perez Rodriguez Leticia , Sauvaget Mélanie , Breuils-Bonnet Sandra , Formoso Karina , Jagana Vineeta , Zhang Shihong , Milara Javier , Cortijo Julio , Turnbull Irene C. , Provencher Steeve , Bonnet Sebastien , Orchando Jordi , Lezoualc’h Frank , Bisserier Malik , Hadri Lahouaria 
Published: September 2024

AbstractBackgroundIdiopathic Pulmonary fibrosis (IPF) is characterized by progressive scarring and fibrosis within the lungs. There is currently no cure for IPF; therefore, there is an urgent need to identify novel therapeutic targets that can prevent the progression of IPF. Compelling evidence indicates that the second messenger, cyclic adenosine monophosphate (cAMP), inhibits lung fibroblast proliferation and differentiation through the classical PKA pathway. However, the contribution of theexchangeprotein directlyactivated bycAMP 1 (Epac1) to IPF pathophysiological processes is yet to be investigated.ObjectiveTo determine the role of the cAMP-binding protein Epac1 in the progression of IPF.MethodsWe used lung samples from IPF patients or healthy controls, mouse lung samples, or lung fibroblast isolated from a preclinical mouse model of PF induced by bleomycin intratracheal injection. The effect of bleomycin (BLM) treatment was determined in Epac1 knock-out mice or wild-type littermates. Epac1 expression was modulatedin vitroby using lentiviral vectors or adenoviruses. The therapeutic potential of the Epac1-selective pharmacological inhibitor, AM-001, was testedin vivoandin vitro,using a bleomycin mouse model of PF and anex vivoprecision-cut lung slices (PCLs) model of human lung fibrosis.ResultsEpac1 expression was increased in the lung tissue of IPF patients, in IPF-diseased fibroblasts and in BLM-challenged mice. Furthermore, Epac1 genetic or pharmacological inhibition with AM-001 decreased normal and IPF fibroblast proliferation and the expression of profibrotic markers, αSMA, TGF-β/SMAD2/3, and interleukin-6 (IL-6)/STAT3 signaling pathways. Consistently, blocking Epac1 protected against BLM-induced lung injury and fibrosis, suggesting a therapeutic effect of Epac1 inhibition on PF pathogenesis and progression. Global gene expression profiling revealed a decrease in the key components of the profibrotic gene signature and neddylation pathway in Epac1-deficient lung fibroblasts and IPF human-derived PLCs. Mechanistically, the protective effect of Epac1 inhibition against PF development involves the inhibition of FoxO3a neddylation and its subsequent degradation by NEDD8, and in part, by limiting the proliferative capacity of lung-infiltrating monocytes.ConclusionsWe demonstrated that Epac1 is an important regulator of the pathological state of fibroblasts in PF and that small molecules targeting Epac1 can serve as novel therapeutic drugs against PF.
Dissecting earthworm diversity in tropical rainforests
Authors: Goulpeau Arnaud , Hedde Mickaël , Ganault Pierre , Lapied Emmanuel , Maggia Marie-Eugénie , Marcon Eric , Decaëns Thibaud 
Published: September 2024

AbstractTropical rainforests are among the most emblematic ecosystems in terms of biodiversity. However, our understanding of the structure of tropical biodiversity is still incomplete, particularly for certain groups of soil organisms such as earthworms, whose importance for ecosystem functioning is widely recognised. This study aims at determining the relative contribution of alpha and beta components to earthworm regional diversity at a hierarchy of nested spatial scales in natural ecosystems of French Guiana. For this, we performed a hierarchical diversity partitioning of a large dataset on earthworm communities, in which DNA barcode-based operational taxonomic units (OTUs) were used as species surrogates. Observed regional diversity comprised 256 OTUs. We found that alpha diversity was lower than predicted by chance, regardless of the scale considered. Community-scale alpha diversity was on average 7 OTUs. Beta diversity among remote landscapes was higher than expected by chance, explaining as much as 87% of regional diversity. This points to regional mechanisms as the main driver of species diversity distribution in this group of organisms with low dispersal capacity. At more local scales, multiplicative beta diversity was higher than expected by chance between habitats, while it was lower than expected by chance between communities in the same habitat. This highlights the local effect of environmental filters on the species composition of communities. The calculation of a Chao 2 index predicts that as much as 1,700 species could be present in French Guiana, which represents a spectacular increase compared with available checklists, and calls into question the commonly accepted estimates of global number of earthworm species.
Optimization of rearingTranseius montdorensisunder laboratory conditions
Authors: Nguyen Hung , Nguyen Binh , Mainali Bishwo , Maselko Maciej 
Published: September 2024

AbstractThe global application ofTranseius montdorensis(Acari: Phytoseiidae) as a biological control agent across various protected crops has proven effective against a range of insect pests like thrips and whiteflies, as well as pest mites like broad mites and russet mites. Optimization of rearingT. montdorensisunder laboratory conditions is crucial for further studies of this species to improve their application in Integrated Pest Management (IPM) programs. Here, we evaluated the development and reproduction ofT. montdorensiswhen fed on four different diets, including cattail pollen (Typha latifolia), living dried fruit mites (Carpoglyphus lactis), frozenC. lactiseggs, and a mixed diet of frozenC. lactiseggs andT. latifoliapollen. Females consuming the mixed diet exhibited superior total fecundity and daily oviposition rate, along with the highest intrinsic rate of increase (rm) and net productive rate (R0) among all diets tested. The immature period was significantly longer for mites on a diet of livingC. lactiscompared to those on other diets. Importantly, utilizing frozenC. lactiseggs andT. latifoliapollen mitigates the risk of infestation and contamination from the living dried fruit mites, which is important for laboratory and field settings when releasing the predator colonies. Our findings not only present an optimized rearing method for predatory mites under laboratory conditions but also suggest potential broader applications for enhancing the effectiveness and sustainability of biological control strategies across various agroecosystems and reducing dependency on chemical pesticides.
Design and immunogenicity of an HIV-1 clade C pediatric envelope glycoprotein stabilized by multiple platforms
Authors: Kumar Sanjeev , del Moral-Sánchez Iván , Singh Swarandeep , Newby Maddy L. , Allen Joel D. , Bijl Tom P. L. , Vaghani Yog , Jing Liang , Ortlund Eric A. , Crispin Max , Patel Anamika , Sanders Rogier W. , Luthra Kalpana 
Published: September 2024

ABSTRACTVarious design platforms are available to stabilize soluble HIV-1 envelope (Env) trimers, which can be used as antigenic baits and vaccine antigens. However, stabilizing HIV-1 clade C trimers can be challenging. Here, we stabilized an HIV-1 clade C trimer based on an Env isolated from a pediatric elite-neutralizer (AIIMS_329) using multiple platforms, including SOSIP.v8.2, ferritin nanoparticles (NP) and an I53-50 two-component NP, followed by characterization of their biophysical, antigenic, and immunogenic properties. The stabilized 329 Envs showed binding affinity to trimer-specific HIV-1 broadly neutralizing antibodies (bnAbs), with negligible binding to non-neutralizing antibodies (non-nAbs). Negative-stain electron microscopy (nsEM) confirmed the native-like conformation of the Envs. Multimerization of 329 SOSIP.v8.2 on ferritin and two-component I53-50 NPs improved the overall affinity to HIV-1 bnAbs and immunogenicity in rabbits. These stabilized HIV-1 clade C 329 Envs demonstrate the potential to be used as antigenic baits and as components of multivalent vaccine candidates in future.
Melanocortin-4 receptor antagonist TCMCB07 alleviates chemotherapy-induced anorexia and weight loss
Authors: Zhu Xinxia , Potterfield Russell , Gruber Kenneth A. , Zhang Emma , Newton Samuel , Norgard Mason A. , Levasseur Peter R. , Bai Peng , Chen Xu , Gu Qingyang , Grossberg Aaron J. , Marks Daniel L. 
Published: September 2024

AbstractCancer patients undergoing chemotherapy often experience anorexia and weight loss that significantly deteriorates overall health, reduces treatment tolerance and quality of life, and worsens oncologic outcomes. There are currently few effective therapeutic options to mitigate these side effects. The central melanocortin system, which plays a pivotal role in regulating appetite and energy homeostasis, presents a logical target for treating anorexia and weight loss. In this preclinical study, we evaluated the efficacy of TCMCB07, a synthetic antagonist of the melanocortin-4 receptor, in mitigating anorexia and weight loss in several rat models of chemotherapy: cisplatin, 5-fluorouracil, cyclophosphamide, vincristine, doxorubicin, and a combination of irinotecan and 5-fluorouracil. Our results indicate that peripheral administration of TCMCB07 improved appetite, stabilized body weight, preserved fat and heart mass, and slightly protected lean mass after multiple cycles of chemotherapy. Furthermore, combining TCMCB07 with a growth differentiation factor 15 antibody enhanced treatment effectiveness. Similar effects from TCMCB07 treatment were observed in a rat tumor model following combination chemotherapy. No significant adverse effects nor increased chemotherapy-related toxicities were observed with TCMCB07 treatment. These findings suggest that peripheral administration of TCMCB07 holds promise as a therapeutic approach for alleviating chemotherapy-induced anorexia and weight loss, potentially benefiting numerous patients undergoing chemotherapy.Graphical abstract
An Experimental Test of Local Adaptation in Native and Introduced Populations of an Ectomycorrhizal Fungus,Suillus luteus
Authors: Allen Brooke M. , Vilgalys Rytas J. , Hoeksema Jason D. 
Published: September 2024

AbstractAfter species introductions and subsequent invasions, organisms often encounter intense selection pressures from biotic and abiotic aspects of novel environments, driving rapid evolutionary changes that potentially lead to local adaptation. This study aimed to investigate how invasion has influenced symbiotic interactions through rapid evolution in exotic isolates of the ectomycorrhizal (EcM) fungusSuillus luteus, which was co-introduced with obligately symbiotic pine trees into the Southern Hemisphere. We conducted a cross-inoculation experiment testing the compatibility of sympatric and allopatric pairings between pines and isolates ofS. luteusfrom native and introduced populations. Our results showed that plant and fungal performance were substantially affected by these pairings, largely supporting a hypothesis of local maladaptation. Several performance metrics indicated stronger outcomes in allopatric pairings compared to sympatric ones. This suggests that fungal isolates may have evolved traits that are less beneficial or even somewhat harmful to their local host plants. These findings highlight the complex dynamics of coevolution and emphasize the necessity of considering both local adaptation and maladaptation in understanding species interactions.
Characterizing the connection between Parkinson’s disease progression and healthcare utilization
Authors: Fitzsimmons Lane , Frau Francesca , Bozzi Sylvie , Chandross Karen J. , Beaulieu-Jones Brett K. 
Published: September 2024

AbstractBackground and ObjectivesParkinson’s disease (PD) progression can be characterized in terms of healthcare utilization by analyzing clinical events across different stages of disease.MethodsPD progression was measured by the Hoehn & Yahr (H&Y) clinical rating scale and clinical events at each stage were evaluated. Natural language processing and a large language model were used to extract H&Y values from real-world data enabling a larger cohort than manually collected studies, and multi-state hidden Markov models were used for H&Y progression likelihood.ResultsWithin the one year, most patients in H&Y stages 2-5 remained in the same stage. Stage transitions, when they occurred, were most frequently to the next higher stage. Higher H&Y stages were associated with discharges into long term care and higher rates of additional clinical events.ConclusionsStratifying key clinical events by H&Y score demonstrates the increases of health care utilization and economic burden with PD severity. Modelling the progression likelihood establishes a progression timeline and emphasizes the unmet need to identify treatment options that stop or slow these transitions.
A rapid, inexpensive, culture-free, universal bacterial identification system using internal transcribed spacer targeting primers: a proof-of-principle study
Authors: Asthana Vishwaratn , Nieves Erika Martínez , Bugga Pallavi , Smith Clara , Dunn Tim , Narayanasamy Satish , Dickson Robert P. , VanEpps J. Scott 
Published: September 2024

ABSTRACTTechniques for bacterial detection and identification can be characterized as either untargeted and taxonomically broad or targeted and taxonomically narrow. Untargeted techniques (e.g., culture and sequencing) are time-consuming and/or expensive while targeted techniques (polymerase chain reaction; PCR) can be faster and less expensive but require a strong pre-test suspicion of the potential organism to choose the correct test. We have developed a universal bacterial identification system that is as taxonomically broad as culture and amplicon sequencing but as fast, easy, and affordable as PCR. The platform utilizes a unique universal polymerase chain reaction (PCR) primer set that targets the internal transcribed spacer (ITS) regions between conserved bacterial genes, creating a distinguishable electrophoretic pattern for each bacterial species. Bioinformatic simulation demonstrates that at least 45 commonly isolated pathogenic species can be uniquely identified from a single set of PCR primers using this approach. We experimentally confirmed these predictions on seven representative human pathogens, including gram-negatives and gram-positives, aerobes and anaerobes, and spore formers. Withouta prioriknowledge of the organism, this system can rapidly identify the unique pattern generated by multiple species in a single reaction. Using quantitative PCR, the system can also determine the corresponding concentration of the organism in question. We also show that the primers are resilient to human DNA contamination at physiologic concentrations, eliminating the need for complex and time intensive extraction methods. Proof-of-principle testing on actual clinical specimens demonstrate that this assay can identify more than twice the species as current multiplex PCR assays (e.g., BioFire) using only one universal primer pair in a single PCR reaction, providing results in <3 hours for <$20 without bioinformatic turnaround time.SIGNIFICANCE STATEMENTThis paper describes a novel bacterial identification system that is as taxonomically broad as culture and amplicon sequencing but as fast, easy, and affordable as PCR. The assay covers more than twice the species as the leading multiplex PCR assays but uses only one universal primer pair in a single PCR reaction. It is resilient to human genomic contamination precluding the need for timely or costly methods to clear human DNA. This approach represents a major advancement in the decades-long struggle to rapidly and accurately identify bacteria.
Free fatty acids accelerate β-cell death in type 1 diabetes
Authors: Elliott Emily C. , Sakar Soumyadeep , Bramer Lisa , Burnet Meagan , Kim Young-Mo , Yi Xiaoyan , Estevao Igor L. , Rewers Marian , Cambronne Xiaolu A. , Vehik Kendra , Arrojo e Drigo Rafael , Metz Thomas O. , Eizirik Decio L. , Webb-Robertson Bobbie-Jo M. , Mirmira Raghavendra G. , Nakayasu Ernesto S. 
Published: September 2024

AbstractType 1 diabetes (T1D) results from autoimmune destruction of the insulin producing pancreatic β cells. The body’s lipid metabolism is strongly regulated during this process but there is a need to understand how this regulation contributes to the β-cell death. Here, we show that fatty acids are released from plasma lipoproteins in children during islet autoimmunity, prior to T1D onset. These fatty acids (FFAs) enhanced cytokine-mediated apoptosis in cultured insulin-producing cells by downregulating the production of nicotinamide adenosine dinucleotide (NAD) via its salvage pathway, as well as deregulated central carbon metabolism and impaired levels of ATP. Downregulation of the NAD salvage pathway and central carbon metabolism enzymes were further observed during T1D development, supporting that the pathways for NAD and energy production are compromisedin vivo. Our findings show that fatty acids are released during islet autoimmunity, accelerating disease development through impaired NAD metabolism.