bluuebunny/crossref_metadata_2025 huggingface dataset:
Lack of the IFN-γ signal leads to lethalOrientia tsutsugamushiinfection in mice with skin eschar lesions
Authors: Liang Yuejin , Wang Hui , Sun Keer , Sun Jiaren , Soong Lynn
Published: February 2024

Scrub typhus is an acute febrile disease due toOrientia tsutsugamushi(Ot) infection and can be life-threatening with organ failure, hemorrhage, and fatality. Yet, little is known as to how the host reacts toOtbacteria at early stages of infection; no reports have addressed the functional roles of type I versus type II interferon (IFN) responses in scrub typhus. In this study, we used comprehensive intradermal (i.d.) inoculation models and two clinically predominantOtstrains (Karp and Gilliam) to uncover early immune events. Karp infection induced sequential expression ofIfnbandIfngin inflamed skin and draining lymph nodes at days 1 and 3 post-infection. Using doubleIfnar1-/-Ifngr1-/-andStat1-/-mice, we found that deficiency in IFN/STAT1 signaling resulted in lethal infection with profound pathology and skin eschar lesions, that resembled to human scrub typhus. Further analyses demonstrated that deficiency in IFN-γ, but not IFN-I, resulted in impaired NK cell and macrophage activation and uncontrolled bacterial growth and dissemination, leading to metabolic dysregulation, excessive inflammatory cell infiltration, and exacerbated tissue damage. NK cells were found to be the major cellular source of early IFN-γ, contributing to the initialOtcontrol. In vitro studies with dendritic cell cultures revealed a superior antibacterial effect offered by IFN-γ than IFN-β. Comparative in vivo studies with Karp- and Gilliam-infection revealed a crucial role of IFN-γ signaling in protection against progression of eschar lesions andOtinfection lethality. Additionally, our i.d. mouse models of lethal infection with eschar lesions are promising tools for immunological study and vaccine development for scrub typhus.

Scrub typhus can lead to severe complications and even fatality if not treated properly; however, the early host immune responses toOtbacterium infection remain unclear. This study focused on the functional roles of IFNs in i.d. inoculation mouse models of scrub typhus. We found that mice lacking IFN receptors were highly susceptible toOtinfection, which resulted in severe pathology and skin eschar lesions that resembled to human scrub typhus. Further investigation revealed that the lack of IFN-γ, but not IFN-I, resulted in dysregulated innate immune responses, leading to uncontrolled bacterial burdens and tissue damage. Using IFN-γ reporter mice and neutralizing antibody treatment, we confirmed that NK cells were the major source of early IFN-γ, and thus played a key role in controllingOtdissemination. Moreover, our comparative studies with twoOtstrains revealed bacterium strain- and dose-dependent eschar formation and disease severity. In conclusion, our study highlights the crucial role of IFN-γ signaling in ensuring host protection againstOtinfection. Our mouse models resemble skin eschar lesions and lethal infections observed in human disease, offering potential for future immunological studies on scrub typhus.
Proliferation of SH-SY5Y neuroblastoma cells on confined spaces
Authors: Kalwarczyk Ewelina , Lukasiak Agnieszka , Woznica Damian , Switlik Weronika , Anchimowicz Julia , Zielonka Piotr , Jakiela Slawomir
Published: February 2024

Background

Microfluidics offers precise drug delivery and continuous monitoring of cell functions, which is crucial for studying the effects of toxins and drugs. Ensuring proper cell growth in these space-constrained systems is essential for obtaining consistent results comparable to standard Petri dishes.

New method

We investigated the proliferation of SH-SY5Y cells on circular polycarbonate chambers with varying surface areas. SH-SY5Y cells were chosen for their relevance in neurodegenerative disease research.

Results

Our study demonstrates a correlation between the chamber surface area and SH-SY5Y cell growth rates. Cells cultured in chambers larger than 10 mm in diameter exhibited growth comparable to standard 60-mm dishes. In contrast, smaller chambers significantly impeded growth, even at identical seeding densities. Similar patterns were observed for HeLaGFP cells, while 16HBE14σcells proliferated efficiently regardless of chamber size. Additionally, SH-SY5Y cells were studied in a 12-mm diameter sealed chamber to assess growth under restricted gas exchange conditions.

Comparison with existing methods

Our findings underscore the limitations of small chamber sizes in microfluidic systems for SH-SY5Y cells, an issue not typically addressed by conventional methods.

Conclusions

SH-SY5Y cell growth is highly sensitive to spatial constraints, with markedly reduced proliferation in chambers smaller than 10 mm. This highlights the need to carefully consider chamber size in microfluidic experiments to achieve cell growth rates comparable to standard culture dishes. The study also shows that while SH-SY5Y and HeLaGFP cells are affected by chamber size, 16HBE14σcells are not. These insights are vital for designing effective microfluidic systems for bioengineering research.
Counterfactual MRI Generation with Denoising Diffusion Models for Interpretable Alzheimer’s Disease Effect Detection
Authors: Dhinagar Nikhil J. , Thomopoulos Sophia I. , Laltoo Emily , Thompson Paul M.
Published: February 2024

Generative AI models have recently achieved mainstream attention with the advent of powerful approaches such as stable diffusion, DALL-E and MidJourney. The underlying breakthrough generative mechanism of denoising diffusion modeling can generate high quality synthetic images and can learn the underlying distribution of complex, high-dimensional data. Recent research has begun to extend these models to medical and specifically neuroimaging data. Typical neuroimaging tasks such as diagnostic classification and predictive modeling often rely on deep learning approaches based on convolutional neural networks (CNNs) and vision transformers (ViTs), with additional steps to help in interpreting the results. In our paper, we train conditional latent diffusion models (LDM) and denoising diffusion probabilistic models (DDPM) to provide insight into Alzheimer’s disease (AD) effects on the brain’s anatomy at the individual level. We first created diffusion models that could generate synthetic MRIs, by training them on real 3D T1-weighted MRI scans, and conditioning the generative process on the clinical diagnosis as a context variable. We conducted experiments to overcome limitations in training dataset size, compute time and memory resources, testing different model sizes, effects of pretraining, training duration, and latent diffusion models. We tested the sampling quality of the disease-conditioned diffusion using metrics to assess realism and diversity of the generated synthetic MRIs. We also evaluated the ability of diffusion models to conditionally sample MRI brains using a 3D CNN-based disease classifier relative to real MRIs. In our experiments, the diffusion models generated synthetic data that helped to train an AD classifier (using only 500 real training scans) -and boosted its performance by over 3% when tested on real MRI scans. Further, we used implicit classifier-free guidance to alter the conditioning of an encoded individual scan to its counterfactual (representing a healthy subject of the same age and sex) while preserving subject-specific image details. From this counterfactual image (where the same person appears healthy), a personalized disease map was generated to identify possible disease effects on the brain. Our approach efficiently generates realistic and diverse synthetic data, and may create interpretable AI-based maps for neuroscience research and clinical diagnostic applications.
NLRP3, NLRP6, and NLRP12 are inflammasomes with distinct expression patterns
Authors: Wei Bo , Billman Zachary P. , Nozaki Kengo , Goodridge Helen S. , Miao Edward A.
Published: February 2024

Inflammasomes are sensors that detect cytosolic microbial molecules or cellular damage, and in response they initiate a form of lytic regulated cell death called pyroptosis. Inflammasomes signal via homotypic protein-protein interactions where CARD or PYD domains are crucial for recruiting downstream partners. Here, we screened these domains from NLR family proteins, and found that the PYD domain of NLRP6 and NLRP12 could activate caspase-1 to induce cleavage of IL-1β and GSDMD. Inflammasome reconstitution verified that full length NLRP6 and NLRP12 formed inflammasomes in vitro, and NLRP6 was more prone to auto-activation. NLRP6 was highly expressed in intestinal epithelial cells (IEC), but not in immune cells. Molecular phylogeny analysis found that NLRP12 was closely related to NLRP3, but the activation mechanisms are different. NLRP3 was highly expressed in monocytes and macrophages, and was modestly but appreciably expressed in neutrophils. In contrast, NLRP12 was specifically expressed in neutrophils and eosinophils, but was not detectable in macrophages. NLRP12 mutations cause a periodic fever syndrome called NLRP12 autoinflammatory disease. We found that several of these patient mutations caused spontaneous activation of caspase-1 in vitro, which likely causes their autoinflammatory disease. Different cell types have unique cellular physiology and structures which could be perturbed by a pathogen, necessitating expression of distinct inflammasome sensors to monitor for signs of infection.
Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis thymoma
Authors: Yasumizu Yoshiaki , Kinoshita Makoto , Zhang Martin Jinye , Motooka Daisuke , Suzuki Koichiro , Okuzaki Daisuke , Nojima Satoshi , Funaki Soichiro , Shintani Yasushi , Ohkura Naganari , Morii Eiichi , Okuno Tatsusada , Mochizuki Hideki
Published: February 2024

Myasthenia gravis (MG) is known to be epidemiologically associated with abnormalities of the thymus, an organ that maintains central tolerance. However, due to the complexity of the thymus, specific characteristics related to the pathogenesis of MG remain elusive. In our study, we attempted to narrow down the features associated with MG using spatial transcriptome analysis of thymoma and thymic hyperplasia samples. We found that the majority of thymomas were constituted by the cortical region, whereas the medullary region was localized in comparatively restricted areas. Moreover, the medullary region contained polygenic enrichment, MG-specific germinal center structures, and a supporting immune microenvironment. Additionally, neuromuscular medullary thymic epithelial cells (nmTECs), previously identified as MG-specific autoantigen-producing cells, were situated at the cortico-medullary junction. The immune microenvironment in the medulla was characterized by a specific chemokine pattern and specific immune cells, such asCCR7+migratory dendritic cells (migDCs) and effector regulatory T (Treg) cells. Furthermore, similar germinal center structures and immune microenvironments were observed in the medulla during thymic hyperplasia. This study indicates that the medulla and junction areas are related to the pathology of MG, suggesting that these areas should be the focus of future studies on MG pathogenesis and drug targeting.
Comparison of Machine Leaning Models for Prediction of Acute Pain Severity and On-Treatment Opioid Utilization in Oral Cavity and Oropharyngeal Cancer Patients Receiving Radiation Therapy: Exploratory Analysis from a Large-Scale Retrospective Cohort
Authors: Salama Vivian , Humbert-Vidan Laia , Godinich Brandon , Wahid Kareem A. , ElHabashy Dina M. , Naser Mohamed A. , He Renjie , Mohamed Abdallah S.R. , Sahli Ariana J. , Hutcheson Katherine A. , Gunn Gary Brandon , Rosenthal David I. , Fuller Clifton D. , Moreno Amy C.
Published: February 2024

Background

Acute pain is a common and debilitating symptom experienced by oral cavity and oropharyngeal cancer (OC/OPC) patients undergoing radiation therapy (RT). Uncontrolled pain can result in opioid overuse and increased risks of long-term opioid dependence. The specific aim of this exploratory analysis was the prediction of severe acute pain and opioid use in the acute on-treatment setting, to develop risk-stratification models for pragmatic clinical trials.

Materials and Methods

A retrospective study was conducted on 900 OC/OPC patients treated with RT during 2017 to 2023. Clinical data including demographics, tumor data, pain scores and medication data were extracted from patient records. On-treatment pain intensity scores were assessed using a numeric rating scale (0-none, 10-worst) and total opioid doses were calculated using morphine equivalent daily dose (MEDD) conversion factors. Analgesics efficacy was assessed based on the combined pain intensity and the total required MEDD. ML models, including Logistic Regression (LR), Support Vector Machine (SVM), Random Forest (RF), and Gradient Boosting Model (GBM) were developed and validated using ten-fold cross-validation. Performance of models were evaluated using discrimination and calibration metrics. Feature importance was investigated using bootstrap and permutation techniques.

Results

For predicting acute pain intensity, the GBM demonstrated superior area under the receiver operating curve (AUC) (0.71), recall (0.39), and F1 score (0.48). For predicting the total MEDD, LR outperformed other models in the AUC (0.67). For predicting the analgesics efficacy, SVM achieved the highest specificity (0.97), and best calibration (ECE of 0.06), while RF and GBM achieved the same highest AUC, 0.68. RF model emerged as the best calibrated model with ECE of 0.02 for pain intensity prediction and 0.05 for MEDD prediction. Baseline pain scores and vital signs demonstrated the most contributed features for the different predictive models.

Conclusion

These ML models are promising in predicting end-of-treatment acute pain and opioid requirements and analgesics efficacy in OC/OPC patients undergoing RT. Baseline pain score, vital sign changes were identified as crucial predictors. Implementation of these models in clinical practice could facilitate early risk stratification and personalized pain management. Prospective multicentric studies and external validation are essential for further refinement and generalizability.
Prognosis of aneurysmal subarachnoid hemorrhage not altered with transatlantic airplane transfer. A bicentric matched case–control study
Authors: Martino Frédéric , Trainel Milan , Guillaume Jessica , Schaffar Aurélien , Escalard Simon , Pons Adrien , Engrand Nicolas
Published: February 2024

Background

The treatment of a ruptured aneurysm, in a center with expertise in aneurysmal subarachnoid hemorrhage (aSAH), is recommended preferably within 24 to 72 hr. We assessed the impact of long-distance aeromedical evacuation in patients presenting aSAH in a remote island without neuro-interventional capacities.

Methods

This was a case–control study of patients with aSAH flown from a French Caribbean island (Guadeloupe) to Paris, France (6750 km), for neuro-interventional and neuro-ICU management and identical patients from the Paris region over a 10-year period (2010 to 2019). The two populations were matched on age, sex, World Federation of Neurological Surgeons score, and Fisher score. The primary outcome was the 1-year modified Rankin Scale (mRS) score divided into two categories: good outcome (mRS 0 to 3) and poor outcome (mRS 4 to 6). A cost study was added.

Results

Among 128 consecutive aSAH transferred from Guadeloupe, 93 could be matched with 93 patients with aSAH from the Paris area. The median [Q1,Q3] time from diagnosis to securing the aneurysm was 48 hr [30,63] in the Guadeloupe group versus 23 [12,24] in the control group (p<0.001). The rate of good clinical outcome (1-year-mRS ≤ 3) was 75% in the Guadeloupe group and 82% in the control group (p=0.1). The groups did not differ in 1-year mortality (18% vs 14%, p=0.5) and duration of mechanical ventilation. However, Guadeloupe patients more frequently required mechanical ventilation (59% vs 38%, p<0.001) and external ventricular drainage (55% versus 39%, p=0.005) than the control group, although the number of hydrocephalus events did not differ. The additional cost of treating a Guadeloupe patient in mainland France was estimated at 7580 euros, or 17% of the estimated cost in Guadeloupe.

Conclusions

Long distance aeromedical evacuation of Guadeloupe patients with aSAH resulted in a 25-hr increase in median embolization time but had no effect on mortality or functional prognosis at 1 year.
First draft genome assembly and characterization of spongeHalisarca dujardiniireveals key components of basement membrane and broad repertoire of aggregation factors
Authors: Borisenko Ilya , Predeus Alexander , Lavrov Andrey , Ereskovsky Alexander
Published: February 2024

How features characteristic of multicellular animals emerged in evolution and how the body plan of particular taxa was shaped are hotspots of modern evolutionary biology. We can get closer to answering them by studying animals that occupy a basal position on the phylogenetic tree, such as sponges (Porifera). We sequenced the genome of the spongeHalisarca dujardiniiusing Oxford Nanopore and Illumina technologies and made an assembly of long reads, followed by polishing with short reads. The resulting assembly had a size of 176 Mb, matching the prediction from the k-mer distribution, and an N50 of about 785 Kb. By analyzing transposable elements in the genomes ofH. dujardiniiand a number of other sponges, we found that a significant portion of the genome (more than half for Demospongiae) is occupied by repeats, most of which are evolutionary young. RNA-seq data were used to predict about 14000 genes in the genome, several times less than in other Demospongiae. By analyzing ortholog groups unique toH. dujardiniiamong sponges and higher invertebrates, we found overrepresented genes related to the extracellular matrix. The extracellular matrix ofH. dujardiniicontains, among others, key basement membrane components such as laminin, nidogen, fibronectin, and collagen IV, for which phylogenetic analysis has confirmed that it belongs to this type of nonfibrillar collagen. In addition, we showed inH. dujardinii14 aggregation factor genes responsible for cell recognition and adhesion. They are organized in a genomic cluster and have at least two types of domains: Calx-beta, responsible for calcium ion binding, and Wreath domain, unique for this type of molecules. Our obtained assembly and annotation will further expand the understanding of genome evolution at the emergence of animal multicellularity, and will serve as a tool to study the regulation of gene expression by modern methods.
Enhancing Plant Photosynthesis using Carbon Dots as Light Converter and Photosensitizer
Authors: Hu Haitao , Cheng Wenbo , Wang Xueyun , Yang Yu , Yu Xuemeng , Ding Jianwei , Lin Yiliang , Zhao Wei , Zhao Qiao , Ledesma-Amaro Rodrigo , Chen Xihan , Liu Junzhong , Yang Chen , Gao Xiang
Published: February 2024

Improving photosynthetic efficiency is pivotal for CO2-based biomanufacturing and agriculture purposes. Despite the progress on photosynthetic biohybrids integrating biocatalysts with synthetic materials, nanomaterials with improved optical and photoelectrochemical properties are still needed to increase the energy-conversion efficiency. Here, we present a novel approach using carbon dots (CDs) as both intracellular photosensitizers and light converters for enhancing solar energy utilization in photosynthetic organisms. The CDs were produced from cyanobacterial biomass and used to convert a broad spectrum of solar irradiation to red light. We demonstrated that the nanosized CDs were incorporated into cyanobacterial cells and transferred light-excited electrons into the photosynthetic electron transfer chain. The biohybrids consisting of the CDs andSynechococcus elongatusexhibited increased growth rates, enhanced activities of both photosystems, and accelerated linear electron transport, compared with the cyanobacterial cells only. The supplementation of the CDs increased CO2-fixation rate and CO2-to-glycerol production by 2.4-fold and 2.2-fold, respectively. Furthermore, the CDs were shown to enhance photosynthesis and promote growth ofArabidopsis thaliana. The fresh weight of plant was increased 1.8-fold by CDs addition. These results reveal that simultaneous photosensitization and spectral modification could substantially improve the efficiency of natural photosynthesis. This study presents CDs as an attractive nanomaterial with great application potential in agriculture and solar-powered biomanufacturing.
Probing PAC1 receptor activation across species with an engineered sensor
Authors: Cola Reto B. , Niethammer Salome N. , Rajamannar Preethi , Gresch Andrea , Bhat Musadiq A. , Assoumou Kevin , Williams Elyse , Hauck Patrick , Hartrampf Nina , Benke Dietmar , Stoeber Miriam , Levkowitz Gil , Melzer Sarah , Patriarchi Tommaso
Published: February 2024

Class-B1 G protein-coupled receptors (GPCRs) are an important family of clinically relevant drug targets that remain difficult to investigate via high-throughput screening and in animal models. Here, we engineered PAClight1P78A, a novel genetically-encoded sensor based on a class-B1 GPCR (the human PAC1 receptor, hmPAC1R) endowed with high dynamic range (ΔF/F0= 1100%), excellent ligand selectivity and rapid activation kinetics (τON= 1.15 sec). To showcase the utility of this tool for in vitro applications, we thoroughly characterized and compared its expression, brightness and performance between PAClight1P78Atransfected and stably-expressing cells. Demonstrating its use in animal models, we show robust expression and fluorescence responses upon exogenous ligand application ex vivo and in vivo in mice, as well as in living zebrafish larvae. Thus, the new GPCR-based sensor can be used for a wide range of applications across the life sciences empowering both basic research and drug development efforts.
Mutant fate in spatially structured populations on graphs: connecting models to experiments
Authors: Abbara Alia , Pagani Lisa , García-Pareja Celia , Bitbol Anne-Florence
Published: February 2024

In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the probability that a mutant will fix. Evolution experiments are beginning to explicitly address the impact of graph structures on mutant fixation. However, the assumptions of evolutionary graph theory differ from the conditions of modern evolution experiments, making the comparison between theory and experiment challenging. Here, we aim to bridge this gap by using our new model of spatially structured populations. This model considers connected subpopulations that lie on the nodes of a graph, and allows asymmetric migrations. It can handle large populations, and explicitly models serial passage events with migrations, thus closely mimicking experimental conditions. We analyze recent experiments in light of this model. We suggest useful parameter regimes for future experiments, and we make quantitative predictions for these experiments. In particular, we propose experiments to directly test our recent prediction that the star graph with asymmetric migrations suppresses natural selection and can accelerate mutant fixation or extinction, compared to a well-mixed population.

Author Summary

Predicting how mutations spread through a population and eventually take over is important for understanding evolution. Complex spatial structures are ubiquitous in natural microbial populations, and can impact the fate of mutants. Theoretical models have been developed to describe this effect. They predict that some spatial structures have mutant fixation probabilities that differ from those of well-mixed populations. Experiments are beginning to probe these effects in the laboratory. However, there is a disconnect between models and experiments, because they consider different conditions. In this work, we connect them through a new model that closely matches experimental conditions. We analyze recent experiments and propose new ones that should allow testing the effects of complex population spatial structures on mutant fate.
Lipoxin A4yields an electrophilic 15-oxo metabolite that mediates FPR2 receptor-independent anti-inflammatory signaling
Authors: Koudelka Adolf , Buchan Gregory J. , Cechova Veronika , O’Brien James P. , Liu Heng , Woodcock Steven R. , Mullett Steven J. , Zhang Cheng , Freeman Bruce A. , Gelhaus Stacy L.
Published: February 2024

The enzymatic oxidation of arachidonic acid is proposed to yield trihydroxytetraene species (termed lipoxins) that resolve inflammation via ligand activation of the formyl peptide receptor, FPR2. While cell and murine models activate signaling responses to synthetic lipoxins, primarily 5S,6R,15S-trihydroxy-7E,9E,11Z,13E-eicosatetraenoic acid (lipoxin A4, LXA4), there are expanding concerns about the biological formation, detection and signaling mechanisms ascribed to LXA4and related di- and tri-hydroxy ω-6 and ω-3 fatty acids. Herein, the generation and actions of LXA4and its primary 15-oxo metabolite were assessed in control, LPS-activated and arachidonic acid supplemented RAW 264.7 macrophages. Despite protein expression of all enzymes required for LXA4synthesis, both LXA4and its 15-oxo-LXA4metabolite were undetectable. Moreover, synthetic LXA4and the membrane permeable 15-oxo-LXA4methyl ester that is rapidly de-esterified to 15-oxo-LXA4, displayed no ligand activity for the putative LXA4receptor FPR2, as opposed to the FPR2 ligand WKYMVm. Alternatively, 15-oxo-LXA4, an electrophilic α,β-unsaturated ketone, alkylates nucleophilic amino acids such as cysteine to modulate redox-sensitive transcriptional regulatory protein and enzyme function. 15-oxo-LXA4activated nuclear factor (erythroid related factor 2)-like 2 (Nrf2)-regulated gene expression of anti-inflammatory and repair genes and inhibited nuclear factor (NF)-κB-regulated pro-inflammatory mediator expression. LXA4did not impact these macrophage anti-inflammatory and repair responses. In summary, these data show an absence of macrophage LXA4formation and receptor-mediated signaling actions. Rather, if LXA4were present in sufficient concentrations, this, and other more abundant mono- and poly-hydroxylated unsaturated fatty acids can be readily oxidized to electrophilic α,β-unsaturated ketone products that modulate the redox-sensitive cysteine proteome via G-protein coupled receptor-independent mechanisms.
Measurements of neurite extension and nucleokinesis in an iPSC-derived model system following microtubule perturbation
Authors: Sébastien Muriel , Paquette Alexandra L , Ferotin Lilian , Hendricks Adam G , Brouhard Gary J
Published: February 2024

In neurons, patterns of different microtubule types are essential for neurite extension and nucleokinesis. Cellular model systems such as rodent primary cultures and induced pluripotent stem cells (iPSC)-derived neurons have provided key insights into how these patterns are created and maintained through the action of microtubule-associated proteins (MAPs), motor proteins, and regulatory enzymes. iPSC-derived models show tremendous promise but lack benchmarking and validation relative to rodent primary cultures. Here we have characterized a recent iPSC-derived model, in which doxycycline-induced expression of Neurogenin-2 drives consistent trans-differentiation into the neuronal state (EBiSC-NEUR1 neurons, referred to as NGN2 neurons below). We developed a suite of open-access, semi-automated methods to measure neurite extension and nucleokinesis of NGN2 neurons, which compare favorably to published data from other models. Then, we challenged NGN2 neurons with a panel of drugs that perturb microtubule physiology. NGN2 neurons extension and nucleokinesis were significantly perturbed by two microtubule-targeting drugs, namely a taxane (paclitaxel) and a vinca alkaloid (DZ-2384). In contrast, inhibition of microtubule severing (spastazoline) or of deacetylation (trichostatin A) had a limited effect on nucleokinesis only. Our results support the primary importance of microtubule dynamics in neuronal development and demonstrate the power of NGN2 neurons as a model system.
Substrate stiffness modulates the emergence and magnitude of senescence phenotypes in dermal fibroblasts
Authors: Starich Bartholomew , Yang Fan , Tanrioven Derin , Kung Heng-Chung , Baek Joanne , Nair Praful R. , Kamat Pratik , Macaluso Nico , Eoh Joon , Han Kyu Sang , Gu Luo , Walston Jeremy , Sun Sean , Wu Pei-Hsun , Wirtz Denis , Phillip Jude M.
Published: February 2024

Cellular senescence is a major driver of aging and disease. Here we show that substrate stiffness modulates the emergence and magnitude of senescence phenotypes after exposure to senescence inducers. Using a primary dermal fibroblast model, we show that decreased substrate stiffness accelerates senescence-associated cell-cycle arrest and regulates the expression of conventional protein-based biomarkers of senescence. We found that the expression of these senescence biomarkers, namely p21WAF1/CIP1and p16INK4aare mechanosensitive and are in-part regulated by myosin contractility through focal adhesion kinase (FAK)-ROCK signaling. Interestingly, at the protein level senescence-induced dermal fibroblasts on soft substrates (0.5 kPa) do not express p21WAF1/CIP1and p16INK4aat comparable levels to induced cells on stiff substrates (4GPa). However, cells expressCDKN1a, CDKN2a,andIL6at the RNA level across both stiff and soft substrates. Moreover, when cells are transferred from soft to stiff substrates, senescent cells recover an elevated expression of p21WAF1/CIP1and p16INK4aat levels comparable to senescence cells on stiff substrates, pointing to a mechanosensitive regulation of the senescence phenotype. Together, our results indicate that the emergent senescence phenotype depends critically on the local mechanical environments of cells and that senescent cells actively respond to changing mechanical cues.
S100A9 Inhibits and Redirects Prion Protein 89-230 Fragment Amyloid Aggregation
Authors: Ziaunys Mantas , Sulskis Darius , Mikalauskaite Kamile , Sakalauskas Andrius , Snieckute Ruta , Smirnovas Vytautas
Published: February 2024

Protein aggregation in the form of amyloid fibrils has long been associated with the onset and development of various amyloidoses, including Alzheimer’s, Parkinson’s or prion diseases. Recent studies of their fibril formation process have revealed that amyloidogenic protein cross-interactions may impact aggregation pathways and kinetic parameters, as well as the structure of the resulting aggregates. Despite a growing number of reports exploring this type of interaction, they only cover just a small number of possible amyloidogenic protein pairings. One such pair is between two neurodegeneration-associated proteins: the pro-inflammatory S100A9 and prion protein, which are known to co-localizein vivo. In this study, we examined their cross-interactionin vitroand discovered that the fibrillar form of S100A9 modulated the aggregation pathway of mouse prion protein 89-230 fragment, while non-aggregated S100A9 also significantly inhibited its primary nucleation process. These results complement previous observations of the pro-inflammatory protein’s role in amyloid aggregation and highlight its potential role against neurodegenerative disorders.
One-step N-terminomics based on isolation of protein N-terminal peptides from LysargiNase digests by tip-based strong cation exchange chromatography
Authors: Morikawa Kazuya , Nishida Hiroshi , Imami Koshi , Ishihama Yasushi
Published: February 2024

We have developed a one-step isolation method for protein N-terminal peptides from LysargiNase digests by pipette tip-based strong cation exchange (SCX) chromatography. This CHAMP-N (CHromatographic AMplification of Protein N-terminal peptides) method using disposable and parallel-processable SCX tips instead of conventional HPLC SCX columns facilitates simple, sensitive and high-throughput N-terminomic profiling without sacrificing the high identification numbers and selectivity achieved by the HPLC-based method. By applying the CHAMP-N method to HEK293T cells, we identified novel cleavage sites for signal and transit peptides, and non-canonical translation initiation sites. Finally, for proteome-wide terminomics, we present a simple and comprehensive N-and C-terminomics platform employing three different tip-based approaches, including CHAMP-N, in which protease digestion and one-step isolation by tip LC are commonly used to achieve complementary terminome coverages.
Anti-drift pose tracker (ADPT): A transformer-based network for robust animal pose estimation cross-species
Authors: Tang Guoling , Han Yaning , Sun Xing , Zhang Ruonan , Han Minghu , Liu Quanying , Wei Pengfei
Published: February 2024

Deep learning-based methods have advanced animal pose estimation, enhancing accuracy and efficiency in quantifying animal behavior. However, these methods frequently experience tracking drift, where noise-induced jumps in body point estimates compromise reliability. Here, we present the Anti-Drift Pose Tracker (ADPT), a transformer-based tool that mitigates tracking drift in behavioral analysis. Extensive experiments across cross-species datasets—including proprietary mouse and monkey recordings and public Drosophila and macaque datasets—demonstrate that ADPT significantly reduces drift and surpasses existing models like DeepLabCut and SLEAP in accuracy. Moreover, ADPT achieved 93.16% identification accuracy for 10 unmarked mice and 90.36% accuracy for freely interacting unmarked mice, which can be further refined to 99.72%, enhancing both anti-drift performance and pose estimation accuracy in social interactions. With its end-to-end design, ADPT is computationally efficient and suitable for real-time analysis, offering a robust solution for reproducible animal behavior studies. The ADPT code is available athttps://github.com/tangguoling/ADPT.
Simultaneous estimation of genotype error and uncalled deletion rates in whole genome sequence data
Authors: Masaki Nobuaki , Browning Sharon R. , Browning Brian L.
Published: February 2024

Genotype data include errors that may influence conclusions reached by downstream statistical analyses. Previous studies have estimated genotype error rates from discrepancies in human pedigree data, such as Mendelian inconsistent genotypes or apparent phase violations. However, uncalled deletions, which generally have not been accounted for in these studies, can lead to biased error rate estimates. In this study, we propose a genotype error model that considers both genotype errors and uncalled deletions when calculating the likelihood of the observed genotypes in parent-offspring trios. Using simulations, we show that when there are uncalled deletions, our model produces genotype error rate estimates that are less biased than estimates from a model that does not account for these deletions. We applied our model to SNVs in 77 sequenced White British parent-offspring trios in the UK Biobank. We use the Akaike information criterion to show that our model fits the data better than a model that does not account for uncalled deletions. We estimate the genotype error rate at SNVs with minor allele frequency > 0.001 in these data to be 3.2 × 10−4(90% CI: [2.8 × 10−4, 6.2 × 10−4]). We estimate that 77% of the genotype errors at these markers are attributable to uncalled deletions (90% CI: [73%, 88%]).

Author summary

A genotype error occurs when the genotype identified through molecular analysis does not match the actual genotype of the individual being analyzed. Because genotype errors can influence downstream statistical results, previous studies have attempted to estimate the rate of genotype errors in a study sample. However, uncalled deletions, which generally have not been accounted for in these studies, can lead to biased error rate estimates. In this study, we formulate a model adjusting for uncalled deletions when estimating genotype error rates. We show that when uncalled deletions are present, this model results in less biased estimates of genotype error rates compared to a model that does not adjust for uncalled deletions. We apply this model to SNVs in 77 sequenced White British parent-offspring trios in the UK Biobank and estimate the genotype error rate and the proportion of genotype errors that are attributable to uncalled deletions at SNVs with minor allele frequency > 0.001.
The neurohormone tyramine stimulates the secretion of an Insulin-Like Peptide from the intestine to modulate the systemic stress response in C. elegans
Authors: Veuthey Tania , Giunti Sebastián , De Rosa María José , Alkema Mark , Rayes Diego
Published: February 2024

The DAF-2/insulin/insulin-like growth factor signaling (IIS) pathway plays an evolutionarily conserved role in regulating reproductive development, lifespan, and stress resistance. InC. elegans, DAF-2/IIS signaling is modulated by an extensive array of insulin-like peptides (ILPs) with diverse spatial and temporal expression patterns. However, the release dynamics and specific functions of these ILPs in adapting to different environmental conditions remain poorly understood. Here, we show that the ILP, INS-3, plays a crucial role in modulating the response to different types of stressors inC. elegans.ins-3mutants display increased resistance to both heat and oxidative stress; however, under favorable conditions, this advantage is countered by slower reproductive development.ins-3expression in both neurons and the intestine is downregulated in response to environmental stressors. Conversely, the neurohormone tyramine, which is released during the acute flight response, triggers an upregulation inins-3expression. Moreover, we found that tyramine negatively impacts environmental stress resistance by stimulating the release of INS-3 from the intestine. The subsequent release of INS-3 systemically activates the DAF-2 pathway, resulting in the inhibition of cytoprotective mechanisms mediated by DAF-16/FOXO and HSF-1. These studies offer mechanistic insights into the brain-gut communication pathway that weighs adaptive strategies to respond to acute and long-term stress scenarios.
Comparison of Prompt Engineering and Fine-Tuning Strategies in Large Language Models in the Classification of Clinical Notes
Authors: Zhang Xiaodan , Talukdar Nabasmita , Vemulapalli Sandeep , Ahn Sumyeong , Wang Jiankun , Meng Han , Bin Murtaza Sardar Mehtab , Leshchiner Dmitry , Dave Aakash Ajay , Joseph Dimitri F. , Witteveen-Lane Martin , Chesla Dave , Zhou Jiayu , Chen Bin
Published: February 2024

The emerging large language models (LLMs) are actively evaluated in various fields including healthcare. Most studies have focused on established benchmarks and standard parameters; however, the variation and impact of prompt engineering and fine-tuning strategies have not been fully explored. This study benchmarks GPT-3.5 Turbo, GPT-4, and Llama-7B against BERT models and medical fellows’ annotations in identifying patients with metastatic cancer from discharge summaries. Results revealed that clear, concise prompts incorporating reasoning steps significantly enhanced performance. GPT-4 exhibited superior performance among all models. Notably, one-shot learning and fine-tuning provided no incremental benefit. The model’s accuracy sustained even when keywords for metastatic cancer were removed or when half of the input tokens were randomly discarded. These findings underscore GPT-4’s potential to substitute specialized models, such as PubMedBERT, through strategic prompt engineering, and suggest opportunities to improve open-source models, which are better suited to use in clinical settings.
SpiDa-MRI, behavioral and (f)MRI data of adults with fear of spiders
Authors: Zhang Mengfan , Karner Alexander , Kostorz Kathrin , Shea Sophia , Steyrl David , Melinscak Filip , Sladky Ronald , Lor Cindy Sumaly , Scharnowski Frank
Published: February 2024

Neuroimaging has greatly improved our understanding of phobic mechanisms. To expand on these advancements, we present data on the heterogeneity of neural patterns in spider phobia combined with various psychological dimensions of spider phobia, using spider-relevant stimuli of various intensities. Specifically, we have created a database in which 49 spider-fearful individuals viewed 225 spider-relevant images in the fMRI scanner and performed behavioral avoidance tasks before and after the fMRI scan. For each participant, the database consists of the neuroimaging part, which includes an anatomical scan, 5 passive-viewing and 2 resting-state functional runs in both raw and preprocessed form, along with associated quality control reports. Additionally, a behavioral section includes self-report questionnaires and avoidance tasks collected in pre- and post-sessions. The dataset is well suited for investigating neural mechanisms of phobias, brain-behavior correlations, and also contributes to the existing phobic neuroimaging datasets with spider-fearful samples.
Reversal of neuronal tau pathology, metabolic dysfunction, and electrophysiological defects via adiponectin pathway-dependent AMPK activation
Authors: McGregor Eric R. , Lasky Danny J. , Rippentrop Olivia J. , Clark Josef P. , Wright Samantha L. G. , Jones Mathew V. , Anderson Rozalyn M.
Published: February 2024

Changes in brain mitochondrial metabolism are coincident with functional decline; however, direct links between the two have not been established. Here, we show that mitochondrial targeting via the adiponectin receptor activator AdipoRon (AR) clears neurofibrillary tangles (NFTs) and rescues neuronal tauopathy-associated defects. AR reduced levels of phospho-tau and lowered NFT burden by a mechanism involving the energy-sensing kinase AMPK and the growth-sensing kinase GSK3b. The transcriptional response to AR included broad metabolic and functional pathways. Induction of lysosomal pathways involved activation of LC3 and p62, and restoration of neuronal outgrowth required the stress-responsive kinase JNK. Negative consequences of NFTs on mitochondrial activity, ATP production, and lipid stores were corrected. Defects in electrophysiological measures (e.g., resting potential, resistance, spiking profiles) were also corrected. These findings reveal a network linking mitochondrial function, cellular maintenance processes, and electrical aspects of neuronal function that can be targeted via adiponectin receptor activation.
Single-cell trait diversity explains niche and fitness differences in aquatic microbial communities
Authors: Fontana Simone , Schmitz Désirée A. , Daniels Michael , Danza Francesco , Röösli Thomas , Bruderer Hannah , Walser Jean-Claude , Dekaezemacker Julien , Escrig Stephane , Meibom Anders , Pomati Francesco , Schreiber Frank
Published: February 2024

Two fundamental questions in ecology are how biodiversity is maintained and how it affects ecosystem functioning. Until now, it has been difficult to study the above mechanisms in natural microbial communities, yet they are important drivers of biogeochemical ecosystem functions. Here, we use a new approach to define and measure biodiversity in complex lake microbial communities (Lake Cadagno, Switzerland) based on the cell-to-cell variation in multiple functionally relevant phenotypic traits. We use stable isotope probing coupled to correlative imaging using confocal laser scanning microscopy (CLSM) and nanometer-scale secondary ion mass spectrometry (NanoSIMS) to obtain morphological (size), physiological (pigments) and metabolic (carbon and nitrogen isotope uptake and sulfur content) traits for a large number of individual cells along the environmental gradient found across lake depth. We show that cell-to-cell trait variation is significantly correlated with cell densities as a proxy for ecosystem functioning, whereas genetic diversity measured at the level of 16S and 18S is not. Our single-cell analysis provides evidence for a simultaneous increase in niche partitioning (measured as increased evenness in pigment composition) and decrease in fitness differences (measured as decreased variability in sulfur content) due to light limitation and competition for nutrients in deep layers of the lake. This leads to a negative relationship between niche and fitness differences. Our results suggest that niche and fitness differences in natural microbial communities can be understood at the level of single-cell traits, providing a mechanistic understanding of the relationship between microbial diversity and ecosystem functioning.
Multi-site Ultrashort Echo Time 3D Phosphorous MRSI repeatability using novel Rosette Trajectory (PETALUTE)
Authors: Alcicek Seyma , Craig-Craven Alexander Richard , Shen Xin , Chiew Mark , Ozen Ali , Sawiak Stephen , Pilatus Ulrich , Emir Uzay E
Published: February 2024

Purpose

This study aims 1) to implement an operator-independent acquisition, reconstruction, and processing pipeline using a novel rosette k-space pattern for UTE31P 3D MRSI and 2) to evaluate the clinical applicability and replicability at different experimental setups.

Methods

A multicenter repeatability study was conducted for the novel UTE31P 3D Rosette MRSI at three institutions with different experimental setups. Non-localized31P MRSI data of 5 healthy subjects at each site were acquired with an acquisition delay of 65 μs and a final resolution of 10 × 10 × 10 mm3in 9 min. Spectra were quantified using the LCModel package. The potential acceleration was achieved using compressed sensing on retrospectively undersampled data. Reproducibility at each site was evaluated using the inter-subject coefficient of variance.

Results

This novel acquisition and advanced processing techniques yielded high-quality spectra and enabled the detection of the critical brain metabolites at three different sites with different hardware specifications. In vivo, feasibility with an acceleration factor of 4 in 6.75 min resulted in a mean Cramér-Rao lower bounds below 20% for PCr, ATPs, PME, and the mean CoV of ATP/PCr resulted in below %20.

Conclusion

We demonstrated that UTE31P 3D Rosette MRSI acquisition, combined with compressed sensing and LCModel analysis, allows patient-friendly, operator-independent, high-resolution31PMRSI to be acquired at clinical setups.
Impaired response to mismatch novelty in the Li2+-pilocarpine rat model of TLE: correlation with hippocampal monoaminergic inputs
Authors: Nascimento Carlos , Guerreiro-Pinto Vasco , Pawlak Seweryn , Caulino-Rocha Ana , Amat-Garcia Laia , Cunha-Reis Diana
Published: February 2024

Novelty detection, crucial to episodic memory formation, is impaired in epileptic patients with mesial temporal lobe resection. Mismatch novelty detection, that activates the hippocampal CA1 area in humans and is vital for memory reformulation and reconsolidation, is also impaired in patients with hippocampal lesions. In this work we investigated the response to mismatch novelty, as occurs with the new location of known objects in a familiar environment, in the Li2+-pilocarpine rat model of TLE and its correlation with hippocampal monoaminergic markers. Animals showing spontaneous recurrent seizures (SRSs) for at least 4 weeks at the time of behavioural testing showed impaired spatial learning in the radial arm maze, as described. Concurrently, SRSs rats displayed impaired exploratory responses to mismatch novelty, yet novel object recognition was not significantly affected in SRSs rats. While the levels of serotonin and dopamine transporters were mildly decreased in hippocampal membranes from SRS rats, the levels on the norepinephrine transporter, tyrosine hydroxylase and dopamine-β-hydroxylase were enhanced, hinting for an augmentation, rather than an impairment in noradrenergic function in SRS animals. Altogether, this reveals that mismatch novelty detection is particularly affected by hippocampal damage associated to the Li2+-pilocarpine model of epilepsy 4-8 weeks after the onset of SRSs and suggests that deficits in mismatch novelty detection may substantially contribute to cognitive impairment in MTLE. As such, behavioural tasks based on these aspects of mismatch novelty may prove useful in the development of cognitive therapy strategies aiming to rescue cognitive deficits observed in epilepsy.