bluuebunny/crossref_metadata_2025 huggingface dataset:
Tigers in North Dakota; Tiger Salamander (Ambystoma tigrinum) eDNA Surveying for Presence in Cattle Ponds
Authors: Showalter Evan R
Published: May 2024

Environmental DNA (eDNA) allows for efficient and convenient data collection using DNA segments to confirm species presence. There is little literature using eDNA to specifically examine tiger salamander presence in North Dakota. I sampled 8 different cattle ponds in Western North Dakota twice each using a set eDNA collection method from the United States Department of Agriculture. After collecting water samples, the filters were sent to Jonah Ventures for DNA extraction and metabarcoding. Samples were incubated, extracted, ran through a first round of Polymerase Chain Reaction (PCR) inspected on agarose gel. Then the amplicons–product of an amplified or replicated piece of DNA, were cleaned, a second round of PCR followed, then the amplicons were cleaned again. Finally sequencing and bioinformatics took place. Salamanders (genusAmbystoma) were detected at 5 of the 8 sites. Average single season Bayesian occupancy point estimate was 0.655 ± (.165), with a detection probability of 0.735± (.156) over the two site visits. Of the covariates including elevation, surface area, and air temperature, air temperature on visit 2 had the best model but still was not significant. There was no significant correlation between any of the covariates and the naïve detections. This method was effective in detecting the genusAmbystoma, however more work and greater sample site variation could elucidate impacts of species level presence absence data.
Scheduled feeding improves sleep in a mouse model of Huntington’s disease
Authors: Chiem Emily , Zhao Kevin , Dell’Angelica Derek , Ghiani Cristina A. , Paul Ketema N. , Colwell Christopher S.
Published: May 2024

Sleep disturbances are common features of neurodegenerative disorders including Huntington’s disease (HD). The sleep and circadian disruptions are recapitulated in animal models, and these models provide the opportunity to evaluate whether circadian interventions can be effective countermeasures for neurodegenerative disease. Time restricted feeding (TRF) interventions successfully improve activity rhythms, sleep behavior and motor performance in mouse models of HD. Seeking to determine if these benefits of scheduled feeding extend to physiological measures of sleep, electroencephalography (EEG) was used to measure sleep/wake states and polysomnographic patterns in adult mice (six mo-old) under TRF andad libfeeding (ALF). With each diet, both male and female wild-type (WT) and bacterial artificial chromosome transgenic (BACHD) mice were evaluated. Our findings show that male, but not female, BACHD mice exhibited significant changes in the temporal patterning of wake and non-rapid eye movement (NREM) sleep. The TRF intervention reduced the inappropriate early morning activity by increasing NREM sleep in the male BACHD mice. In addition, the scheduled feeding reduced sleep fragmentation (# bouts) in the male BACHD mice. The phase of the rhythm in rapid-eye movement (REM) sleep was significantly altered by the scheduled feeding. The treatment did impact the power spectral curves during the day in male but not female mice. Sleep homeostasis, as measured by the response to six hours of gentle handling, was not altered by the diet. Thus, TRF improves the temporal patterning and fragmentation of NREM sleep without impacting sleep homeostasis. This work adds critical support to the view that sleep is a modifiable risk factor in neurodegenerative diseases.
StereoMM: A Graph Fusion Model for Integrating Spatial Transcriptomic Data and Pathological Images
Authors: Luo Bingying , Teng Fei , Tang Guo , Chen Weixuan , Qu Chi , Liu Xuanzhu , Liu Xin , Liu Xing , Huang Huaqiang , Feng Yu , Zhang Xue , Jian Min , Li Mei , Xi Feng , Li Guibo , Liao Sha , Chen Ao , Xu Xun , Zhang Jiajun
Published: May 2024

Spatially resolved omics technologies generating multimodal and high-throughput data lead to the urgent need for advanced analysis to allow the biological discoveries by comprehensively utilizing information from multi-omics data. The H&E image and spatial transcriptomic data indicate abundant features which are different and complementary to each other. AI algorithms can perform nonlinear analysis on these aligned or unaligned complex datasets to decode tumoral heterogeneity for detecting functional domain. However,the interpretability of AI-generated outcomes for human experts is a problem hindering application of multi-modal analysis in clinic. We presented a machine learning based toolchain called StereoMM, which is a graph fusion model that can integrate gene expression, histological images, and spatial location. StereoMM firstly performs information interaction on transcriptomic and imaging features through the attention module, guaranteeing explanations for its decision-making processes. The interactive features are input into the graph autoencoder together with the graph of spatial position, so that multimodal features are fused in a self-supervised manner. Here, StereoMM was subjected to mouse brain tissue, demonstrating its capability to discern fine tissue architecture, while highlighting its advantage in computational speed. Utilizing data from Stereo-seq of human lung adenosquamous carcinoma and 10X Visium of human breast cancer, we showed its superior performance in spatial domain recognition over competing software and its ability to reveal tumor heterogeneity. The fusion approach for imaging and gene expression data within StereoMM aids in the more accurate identification of domains, unveils critical molecular features, and elucidates the connections between different domains, thereby laying the groundwork for downstream analysis.
Time-lapse Image Super-resolution Neural Network with Reliable Confidence Quantification for Optical Microscopy
Authors: Qiao Chang , Liu Shuran , Wang Yuwang , Xu Wencong , Geng Xiaohan , Jiang Tao , Zhang Jingyu , Meng Quan , Qiao Hui , Li Dong , Dai Qionghai
Published: May 2024

Single image super-resolution (SISR) neural networks for optical microscopy have shown great capability to directly transform a low-resolution (LR) image into its super-resolution (SR) counterpart, enabling low-cost long-term live-cell SR imaging. However, when processing time-lapse data, current SISR models failed to exploit the important temporal dependencies between neighbor frames, often resulting in temporally inconsistent outputs. Besides, SISR models are subject to inference uncertainty that is hard to accurately quantify, therefore it is difficult to determine to what extend can we trust the inferred SR images. Here, we first build a large-scale, high-quality fluorescence microscopy dataset for the time-lapse image super-resolution (TISR) task, and conducted a comprehensive evaluation on two essential components of TISR neural networks, i.e., propagation and alignment. Second, we devised a deformable phase-space alignment (DPA) based TISR neural network (DPA-TISR), which adaptively enhances the cross-frame alignment in the phase domain and outperforms existing state-of-the-art SISR and TISR models. Third, we combined the Bayesian training scheme and Monte Carlo dropout with DPA-TISR, developing Bayesian DPA-TISR, and designed an expected calibration error (ECE)minimization framework to obtain a well-calibrated confidence map along with each output SR image, which reliably implicates potential inference errors. We demonstrate the unique characteristics of Bayesian DPA-TISR underlie the ultralong-term live-cell SR imaging capability with high spatial fidelity, superb temporal consistency, and accurate confidence quantification on a wide variety of bioprocesses.
PrediRep: Modelling hierarchical predictive coding with an unsupervised deep learning network
Authors: Hashim Ibrahim C , Senden Mario , Goebel Rainer
Published: May 2024

Hierarchical predictive coding (hPC) proposes that the cortex continuously generates predictions of incoming sensory stimuli. Deep neural networks inspired by hPC are frequently used to probe the neurocomputational mechanisms suggested by the theory in silico and to generate hypotheses for experimental investigations. However, these networks often deviate from hPC by prioritizing computational efficiency over alignment with its principles. To remedy this, we introduce PrediRep, a deep learning model explicitly designed to emphasize alignment with the theory. PrediRep incorporates the principles of hPC found in the other networks, while avoiding their deviations from it. We evaluate the performance of PrediRep on a next-frame prediction task and its functional alignment with hPC, comparing it to other contemporary deep learning networks inspired by the theory. Our findings demonstrate that PrediRep achieves the closest functional alignment with hierarchical predictive coding without sacrificing computational performance.
Accounting for Cellular-Level Variation in Lysis: Implications for Virus-Host Dynamics
Authors: Dominguez-Mirazo Marian , Harris Jeremy D. , Demory David , Weitz Joshua S.
Published: May 2024

Viral impacts on microbial populations depend on interaction phenotypes - including viral traits spanning adsorption rate, latent period, and burst size. The latent period is a key viral trait in lytic infections. Defined as the time from viral adsorption to viral progeny release, the latent period of bacteriophage is conventionally inferred via one-step growth curves in which the accumulation of free virus is measured over time in a population of infected cells. Developed more than 80 years ago, one-step growth curves do not account for cellular-level variability in the timing of lysis, potentially biasing inference of viral traits. Here, we use nonlinear dynamical models to understand how individual-level variation of the latent period impacts virus-host dynamics. Our modeling approach shows that inference of latent period via one-step growth curves is systematically biased - generating estimates of shorter latent periods than the underlying population-level mean. The bias arises because variability in lysis timing at the cellular level leads to a fraction of early burst events which are interpreted, artefactually, as an earlier mean time of viral release. We develop a computational framework to estimate latent period variability from joint measurements of host and free virus populations. Our computational framework recovers both the mean and variance of the latent period within simulated infections including realistic measurement noise. This work suggests that reframing the latent period as a distribution to account for variability in the population will improve the study of viral traits and their role in shaping microbial populations.

Importance

Quantifying viral traits – including the adsorption rate, burst size, and latent period – is critical to characterize viral infection dynamics and to develop predictive models of viral impacts across scales from cells to ecosystems. Here, we revisit the gold standard of viral trait estimation – the one-step growth curve – to assess the extent to which assumptions at the core of viral infection dynamics lead to ongoing and systematic biases in inferences of viral traits. We show that latent period estimates obtained via one-step growth curves systematically under-estimate the mean latent period and, in turn, over-estimate the rate of viral killing at population scales. By explicitly incorporating trait variability into a dynamical inference framework that leverages both virus and host time series we provide a practical route to improve estimates of the mean and variance of viral traits across diverse virus-microbe systems.
Differential effects of PDE4A5 on cAMP-dependent forms of long-term potentiation
Authors: Tadinada Satya Murthy , Walsh Emily N. , Mukherjee Utsav , Abel Ted
Published: May 2024

cAMP signaling is critical for memory consolidation and certain of forms long-term potentiation (LTP). Phosphodiesterases (PDEs), enzymes that degrade the second messenger cAMP and cGMP, are highly conserved during evolution and represent a unique set of drug targets, given the involvement of these enzymes in several pathophysiological states including brain disorders. The PDE4 family of cAMP selective PDEs, exert regulatory roles in memory and synaptic plasticity, but the specific roles of distinct PDE4 isoforms in these processes are poorly understood. Building on our previous work demonstrating that spatial and contextual memory deficits were caused by expressing selectively the long isoform of the PDE4A subfamily, PDE4A5, in hippocampal excitatory neurons, we now investigate the effects of PDE4A isoforms on different cAMP-dependent forms of LTP. We find that PDE4A5 impairs long-lasting LTP induced by theta burst stimulation (TBS) while sparing long-lasting LTP induced by spaced 4-train stimulation (4X100Hz). This effect requires the unique N-terminus of PDE4A5 and is specific to this long isoform. Targeted overexpression of PDE4A5 in area CA1 is sufficient to impair TBS-LTP, suggesting that cAMP levels in the postsynaptic neuron are critical for TBS-LTP. Our results shed light on the inherent differences among the PDE4A subfamily isoforms, emphasizing the importance of the long isoforms, which have a unique N-terminal region. Advancing our understanding of the function of specific PDE isoforms will pave the way for developing isoform-selective approaches to treat the cognitive deficits that are debilitating aspects of psychiatric, neurodevelopmental, and neurodegenerative disorders.

Key Points

Hippocampal overexpression of a PDE4A subfamily long isoform, PDE4A5, but not a short isoform PDE4A1, impairs spatial and contextual fear memory and the N-terminus of PDE4A5 is important for this effect.

Hippocampal overexpression of PDE4A isoforms, PDE4A1 and PDE4A5 do not impair LTP induced by spaced tetanic stimulation at the CA3-CA1 synapses.

Hippocampal overexpression of PDE4A5, but not PDE4A1 or the N-terminus truncated PDE4A5 (PDE4A5Δ4) selectively impairs LTP induced by theta burst stimulation (TBS) at the CA3-CA1 synapses and expression of PDE4A5 in area CA1 is sufficient for the TBS-LTP deficit.

These results suggest that PDE4A5, through its N-terminus, regulates cAMP pools that are critical for memory consolidation and expression of TBS-LTP at the CA3-CA1 synapses.

GRAPHICAL ABSTRACT

Spaced tetanic stimulation and TBS induce cAMP synthesis and activation of PKA to promote signaling cascades that facilitate expression of long-lasting LTP at the CA3-CA1 synapses. PDE4A5 overexpression in the hippocampus selectively impairs cAMP and PKA dependent TBS-LTP at the CA3-CA1 synapses, while sparing LTP induced by spaced tetanization.
A Comprehensive Model to Differentiate Spontaneous, Drug-induced, and CSCs-related Drug Resistance
Authors: Zheng Kaixin
Published: May 2024

Drug resistance is a pivotal research area in oncology research, yet the integration of multiple sources of resistance into the evolution of drug resistance remains elusive. This study investigates dynamics of drug resistance in chemotherapy utilizing a mathematical model given a treatment protocol. The model categorizes drug resistance into spontaneous, drug-induced, and cancer stem cells (CSCs)-related types. Introducing a novel mathematical framework, this study incorporates explicit dosage-dependent terms to design tailored treatment strategies. A comparative analysis contrasts continuous constant therapy with periodic bolus injection. Virtual patients’ survival times are assessed under baseline dosages for both therapies, revealing the interplay between constant dosage in continuous therapy and maximum dosage in bolus injection on survival time. Our findings demonstrate that, at equivalent cumulative dosages, bolus injection markedly extends patient survival. Furthermore, a potentially bimodal relationship emerges between bolus injection efficacy and maximum dosage, suggesting that two optimal bolus injection strategies may hold.
Spleen tyrosine kinase inhibition mitigates hemin-induced thromboinflammation in the lung and kidney of sickle cell mice
Authors: El-Awaisi Juma , Perrella Gina , Mayor Nicolas , Tinkova Veronika , Cleary Simon J , Grygielska Beata , Watson Steve P , Dimitrov Jordan D , Brill Alexander , Nicolson Phillip LR , Kavanagh Dean , Kalia Neena , Rayes Julie
Published: May 2024

Sickle cell disease (SCD) leads to hemolytic anemia, vaso-occlusive crisis (VOC), hypoperfusion, and progressive organ damage. Hemin, released during hemolysis in SCD, induces platelet activation through CLEC-2, endothelial activation through TLR4, neutrophil adhesion and NETosis, all of which are regulated by spleen tyrosine kinase (Syk). In this study, we assessed neutrophil and platelet recruitment to the pulmonary, renal, splenic, and hepatic microvasculature in control and SCD mice following hemin injection and the effect of Syk inhibition on cell recruitment and organ perfusion. Compared to controls, SCD mice exhibited higher baseline neutrophil and platelet recruitment to the lungs without alterations in lung perfusion as measured by laser speckle contrast imaging. Injection of hemin increased cell recruitment to the pulmonary and renal vasculature with a concomitant reduction in organ perfusion. However, hemin injection did not change cell recruitment or organ perfusion in the spleen and liver, both of which were altered at baseline in SCD mice. Pretreatment of SCD mice with the Syk inhibitor BI-1002494 mitigated baseline and hemin-induced neutrophil and platelet adhesion in the pulmonary and renal microvasculature, with a corresponding normalization of perfusion. Syk regulates vascular integrity in the lung of SCD mice; whilst high concentrations of BI-1002494 increased bleeding, lowering drug concentrations preserved the inhibitory effect on platelet and neutrophil recruitment and lung perfusion and protected from bleeding complications. These data substantiate Syk as a mediator of vascular thrombo-inflammation and hypoperfusion in the lung and kidney of SCD and provide a rationale for pharmacological inhibition as a therapeutic strategy.
Velocity-selective arterial spin labelling bolus duration measurements: Implications for consensus recommendations
Authors: Driver Ian D , Chandler Hannah L , Patitucci Eleonora , Morgan Emma L , Murphy Kevin , Zappala Stefano , Wise Richard G , Germuska Michael
Published: May 2024

Velocity-selective arterial spin labelling (VSASL) MRI is insensitive to arterial transit time. This is an advantage over other perfusion measurements, where long arterial transit times can lead to bias. Therefore, VSASL can be used to study perfusion in the presence of long arterial transit times, such as in the ageing brain, in vascular pathologies, and cancer, or where arterial transit time changes, such as during measurement of cerebrovascular reactivity (CVR). However, when calculating perfusion (cerebral blood flow, CBF, in the brain) from VSASL signal, it is assumed that images are acquired before the trailing edge of the labelled blood has arrived in the imaging slice. The arrival of the trailing edge of the labelled bolus of blood will cause an underestimation of perfusion. Here we measure bolus duration in young, healthy human brains, both at rest and during elevated CBF. Grey matter bolus duration was 1.61 ± 0.31 s, but there was a large spatial heterogeneity, with bolus duration being lower in anterior brain regions, with some areas having bolus duration < 1.2 s. We place these results in context of recommendations from a recent consensus paper, which recommends imaging 1.4 s after the label, potentially underestimating CBF in anterior regions. Further, we observed a 0.23 ± 0.12 s reduction in grey matter bolus duration with 5% CO2inhalation. These results can be used to inform the experimental design of future VSASL studies, to avoid underestimating perfusion by imaging after the arrival of the trailing edge of the labelled bolus.
COEXIST: Coordinated single-cell integration of serial multiplexed tissue images
Authors: Heussner Robert T. , Watson Cameron F. , Eddy Christopher Z. , Wang Kunlun , Cramer Eric M. , Creason Allison L. , Mills Gordon B. , Chang Young Hwan
Published: May 2024

Multiplexed tissue imaging (MTI) and other spatial profiling technologies commonly utilize serial tissue sectioning to comprehensively profile samples by imaging each section with unique biomarker panels or assays. The dependence on serial sections is attributed to technological limitations of MTI panel size or incompatible multi-assay protocols. Although image registration can align serially sectioned MTIs, integration at the single-cell level poses a challenge due to inherent biological heterogeneity. Existing computational methods overlook both cell population heterogeneity across modalities and spatial information, which are critical for effectively completing this task. To address this problem, we first use Monte-Carlo simulations to estimate the overlap between serial 5μm-thick sections. We then introduce COEXIST, a novel algorithm that synergistically combines shared molecular profiles with spatial information to seamlessly integrate serial sections at the single-cell level. We demonstrate COEXIST necessity and performance across several applications. These include combining MTI panels for improved spatial single-cell profiling, rectification of miscalled cell phenotypes using a single MTI panel, and the comparison of MTI platforms at single-cell resolution. COEXIST not only elevates MTI platform validation but also overcomes the constraints of MTI’s panel size and the limitation of full nuclei on a single slide, capturing more intact nuclei in consecutive sections and thus enabling deeper profiling of cell lineages and functional states.
The Jag2/Notch1 signaling axis promotes sebaceous gland differentiation and controls progenitor proliferation
Authors: Abidi Syeda Nayab Fatima , Chan Sara , Seidel Kerstin , Lafkas Daniel , Vermeulen Louis , Peale Frank , Siebel Christian W.
Published: May 2024

The sebaceous gland (SG) is a vital appendage of the epidermis, and its normal homeostasis and function is crucial for effective maintenance of the skin barrier. Notch signaling is a well-known regulator of epidermal differentiation, and has also been shown to be involved in postnatal maintenance of SGs. However, the precise role of Notch signaling in regulating SG differentiation in the adult homeostatic skin remains unclear. While there is evidence to suggest that Notch1 is the primary Notch receptor involved in regulating the differentiation process, the ligand remains unknown. Using monoclonal therapeutic antibodies designed to specifically inhibit of each of the Notch ligands or receptors, we have identified the Jag2/Notch1 signaling axis as the primary regulator of sebocyte differentiation in homeostatic skin. Mature sebocytes are lost upon specific inhibition of the Jag2 ligand or Notch1 receptor, resulting in the accumulation of proliferative stem/progenitor cells in the SG. Strikingly, this phenotype is reversible, as these stem/progenitor cells re-enter differentiation when the inhibition of Notch activity is lifted. Thus, Notch activity promotes correct sebocyte differentiation, and is required to restrict progenitor proliferation.
Analysis of time-to-positivity data in tuberculosis treatment studies: Identifying a new limit of quantification
Authors: Dufault Suzanne M. , Davies Geraint R. , Svensson Elin M. , Sloan Derek J. , McCallum Andrew D. , Patel Anu , Van Brantegem Pieter , Denti Paulo , Phillips Patrick P. J.
Published: May 2024

The BACTEC Mycobacteria Growth Indicator Tube (MGIT) machine is the standard globally for detecting viable mycobacteria in patients’ sputum. Samples are observed for no longer than 42 days, at which point the sample is declared “negative” for tuberculosis (TB). This time to detection of bacterial growth, referred to as time-to-positivity (TTP), is increasingly of interest not solely as a diagnostic tool, but as a continuous biomarker wherein change in TTP over time can be used for comparing the bactericidal activity of different TB treatments. However, as a continuous measure, there are oddities in the distribution of TTP values observed, particularly at higher values. We explored whether there is evidence to suggest setting an upper limit of quantification (ULOQM) lower than the diagnostic limit of detection (LOD) using data from several TB-PACTS randomized clinical trials and PanACEA MAMS-TB. Across all trials, less than 7.1% of all weekly samples returned TTP measurements between 25 and 42 days. Further, the relative absolute prediction error (%) was highest in this range. When modeling with ULOQMs of 25 and 30 days, the precision in estimation improved for 23 of 25 regimen-level slopes as compared to models using the diagnostic LOD while also improving the discrimination between regimens based on Bayesian posteriors. While TTP measurements between 25 days and the diagnostic LOD may be important for diagnostic purposes, TTP values in this range may not contribute meaningfully to its use as a quantitative measure, particularly when assessing treatment response, and may lead to under-powered clinical trials.

Highlights

The BACTEC Mycobacteria Growth Indicator Tube (MGIT) machine is the STAND, PaMZard globally for the detection and diagnosis of tuberculosis.

As MGIT machine use becomes more ubiquitous, its time-to-positivity (TTP) measures are increasingly of interest as a continuous biomarker for evaluating bactericidal activity of TB treatment regimens.

Using data from seven previously published trials, this work highlights the evidence for setting a limit of quantification for quantitative analyses that is below the diagnostic limit of detection. TTP values near the upper limit of detection appear to be noisier and sparser, with precision improving for estimation of 23 of 25 regimen-specific rates of change in TTP when analyzed with a lower limit of quantification.

While TTP measurements between 25 days and the diagnostic LOD may be important for diagnostic purposes, TTP values in this range may not contribute meaningfully to its use as a quantitative measure, particularly when assessing early treatment response.
Prevalence and determinants of scabies: a global systematic review and meta-analysis
Authors: GUPTA SAPTORSHI , Thornley Simon , Morris Arthur , Sundborn Gerhard , Grant Cameron
Published: May 2024

Background Scabies is a neglected skin disease that disproportionately affects people from resource poor and overcrowded countries. Global data on prevalence and risk factors are limited. Methods Databases (PubMed, Scopus and Google Scholar) were accessed to identify observational studies about scabies published between 2000 and 2023. Results were pooled to estimate prevalence and identify factors which explained between-study heterogeneity. Odds ratios, risk of bias, subgroup analyses and meta-regression were used to describe variation in effect size and heterogeneity based on country-level demographic and economic variables. Findings Fifty-four studies yielded a pooled prevalence of 14.0% (95% confidence interval [CI] 11.4-17.1%) with substantial heterogeneity (I^2=100%; τ^2=0.77). Prevalence was higher in Oceania (18.2%; 95% CI 14.1-23.1) compared to other regions. Pooled risk factors for scabies showed significant associations for behavioral factors including contact with someone with itch (odds ratio [OR] 9.26; 95% CI 2.94-29.2), no use of soap (OR 3.42; 95% CI 2.80-4.18), infrequent bathing (OR 2.68; 95% CI 1.76- 4.08), bed-sharing (OR 2.57; 95% CI 1.33-4.96), clothes sharing (OR 2.40; 95% CI 1.39- 4.13), treated water source (OR 2.29; 95% CI 1.67-3.15) and presence of pets (OR 2.19; 95% CI 1.54-3.11). Socio-economic factors were not convincingly associated with scabies prevalence. Conclusion Prevalence of scabies is associated with geographic location and behavioural factors, but not between-country socioeconomic status. This study identifies risk factors for which targeted behavioural interventions addressing interpersonal interaction, personal hygiene practices and specific treatments related to scabies create the potential to reduce scabies disease burden.
Inotropes and mortality in patients with cardiogenic shock: An instrumental variable analysis from the SWEDEHEART registry
Authors: Petursson Petur , Gudmundsson Thorsteinn , Råmunddal Truls , Angerås Oskar , Rawshani Araz , Mohammad Moman A. , Persson Jonas , Alfredsson Joakim , Hofmann Robin , Jernberg Tomas , Fröbert Ole , Erlinge David , Redfors Björn , Omerovic Elmir
Published: May 2024

Background

The use of inotropic agents in treating cardiogenic shock (CS) remains controversial. We aimed to investigate the effect of treatment with inotropes on 30-day mortality in patients with CS from the SWEDEHEART registry (The Swedish Web-system for Enhancement and Development of Evidence-based care in Heart disease Evaluated According to Recommended Therapies).

Methods

We used data from the national SWEDEHEART registry on all patients diagnosed with CS in Sweden between 2000 and 2022. The primary endpoint was 30-day all-cause mortality. We used multilevel Cox proportional-hazards regression with instrumental variable and inverse probability weighting propensity score to adjust for known and unknown confounders. The treatment-preference instrument was the quintile of preference for using inotropes at the treating hospital.

Results

In total, 16,214 patients (60.5% men and 39.5% women) were included; 23.5% had diabetes, 10.2% had a previous myocardial infarction (MI), and 13.8% had previous heart failure (HF). The median age was 70 years (interquartile range; 19), and 66.4% were >70. Acute coronary syndrome (ACS) was the cause of CS in 82.9% of patients. Inotropic agents were used in 43.8% of patients, while 56.2% did not receive inotropic agents. There were 7,875 (48.1%) deaths. On average, patients treated with inotropes were two years younger and more likely to have ACS. Patients not treated with inotropes were more likely to have previous MI and previous PCI but less likely to undergo PCI. The number of patients with CS decreased by 12% per year (Ptrend<0.001). There was a considerable variation between hospitals in the preference for using inotropes ranging from 25 to 78% (P<0.001). Inotropes increased by 5% per year (Ptrend<0.001). The unadjusted mortality in CS increased by 2% per calendar year (Ptrend<0.001). The risk of death was higher in patients treated with inotropes [adjusted hazard ratio (HRadj) 1.72; 95% confidence interval (CI) 1.26-2.35; P=0.001]. There was a quantitative interaction between inotrope treatment and age and diagnosis (Pinteraction< 0.001 and Pinteraction= 0.018, respectively).

Conclusions

In this observational study, using inotropes was associated with a higher mortality risk in patients with CS. The increased risk of death was more pronounced in patients younger than 70. The number of patients with CS is decreased, while the use of inotropes and mortality increased in Sweden.
Insulin regulates lymphatic endothelial function via palmitoylation
Authors: Gonzalez-Nieves Silvia , Wei Xiaochao , McQuillan Jay , Zhang Qiang , Zhang Jinsong , McGuffee Reagan M. , Ford David A. , Love-Gregory Latisha , Abumrad Nada A. , Gelman Andrew E , Semenkovich Clay F. , Cifarelli Vincenza
Published: May 2024

Lipid metabolism plays a critical role in lymphatic endothelial cell (LEC) development and maintenance. Altered lipid metabolism is associated with loss of lymphatic vessel integrity, which compromises organ function, protective immunity, and metabolic health. However, the role of lipid metabolism in LEC function is not well understood.

Insulin is a key regulator of lipid metabolism and protein palmitoylation, the reversible post-translational protein modification by palmitate that affects protein stability, trafficking, protein-protein, and protein-membrane interactions. Human LECs are highly sensitive to insulin and can develop insulin resistancein vitro, but whether insulin regulates LEC protein palmitoylation and function is unknown.

To examine the role of palmitoylation in LEC function, we generated the first palmitoylation proteomics profile in human LECs, validated insulin regulated targets and profiled differences in palmitoylation between lymphatic and blood endothelial cells. Palmitoylation occurred primarily in proteins involved in LEC vesicular or membrane trafficking, translation initiation, and in those found in membrane rafts. Insulin enriched palmitoylation of LEC proteins involved in GTPase signaling, ubiquitination, and junctional anchoring. We also determined that the long-chain fatty acid receptor CD36 mediates optimal lymphatic palmitoylation. CD36 silencing in LECs doubled palmitoylation targets involving proteins related to inflammation and neutrophil degranulation contributing to anactivatedinflamed endothelium. These results suggest that the coordination of the process of palmitoylation is critical for normal lymphatic endothelial function.
HisCl1regulates gustatory habituation in sweet taste neurons and mediates sugar ingestion inDrosophila
Authors: Kim Haein , Zhong Ziqing , Cui Xinyue , Sung Hayeon , Agrawal Naman , Jiang Tianxing , Dus Monica , Yapici Nilay
Published: May 2024

Similar to other animals, the fly,Drosophila melanogaster, reduces its responsiveness to tastants with repeated exposure, a phenomenon called gustatory habituation. Previous studies have focused on the circuit basis of gustatory habituation in the fly chemosensory system1,2. However, gustatory neurons reduce their firing rate during repeated stimulation3, suggesting that cell-autonomous mechanisms also contribute to habituation. Here, we used deep learning-based pose estimation and optogenetic stimulation to demonstrate that continuous activation of sweet taste neurons causes gustatory habituation in flies. We conducted a transgenic RNAi screen to identify genes involved in this process and found that knocking downHistamine-gated chloride channel subunit 1(HisCl1)in the sweet taste neurons significantly reduced gustatory habituation. Anatomical analysis showed thatHisCl1is expressed in the sweet taste neurons of various chemosensory organs. Using single sensilla electrophysiology, we showed that sweet taste neurons reduced their firing rate with prolonged exposure to sucrose. Knocking downHisCl1in sweet taste neurons suppressed gustatory habituation by reducing the spike frequency adaptation observed in these neurons during high-concentration sucrose stimulation. Finally, we showed that flies lackingHisCl1in sweet taste neurons increased their consumption of high-concentration sucrose solution at their first meal bout compared to control flies. Together, our results demonstrate that HisCl1 tunes spike frequency adaptation in sweet taste neurons and contributes to gustatory habituation and food intake regulation in flies. Since HisCl1 is highly conserved across many dipteran and hymenopteran species, our findings open a new direction in studying insect gustatory habituation.
TAK1 operates at the primary cilium in non-canonical TGFB/BMP signaling to control heart development
Authors: Doganli Canan , Baird Daniel A. , Ali Yeasmeen , Thomsen Oskar Kaaber , Audain Enrique , Jessen Line , Truelsen Pauline Munck , Mogensen Johanne Bay , Holm Maria Schrøder , Apolínová Kateřina , Buttò Lorenzo , Diamanti Maria , Fialová Jindřiška Leischner , Wade Emma M. , Robertson Stephen P. , Pedersen Lotte Bang , Argiro Laurent , Lescroart Fabienne , Hitz Marc-Phillip , Christensen Søren Tvorup , Larsen Lars Allan
Published: May 2024

Transforming Growth Factor-Beta-Activated Kinase 1 (TAK1/MAP3K7), along with its upstream regulators TAK1-Binding Protein 2 (TAB2) and the catalytic alpha-subunit of Protein Kinase A (PKA-Cα/PRKACA), has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease (CHD) and rare variants in PKA-Cα and TAK1 cause cardioacrofacial dysplasia (CAFD), and Frontometaphyseal Dysplasia (FMD) and cardiospondylocarpofacial syndrome (CSCFS), respectively, rare multisystem syndromes, where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1,471 CHD patients with extracardiac anomalies (syndromic CHD, sCHD), 2,405 patients with nonsyndromic CHD (nsCHD) and 45,082 controls showed increased burden of rareTAB2andTAK1variants in sCHD, but not in nsCHD. Detailed characterization oftak1-/-andtab2-/-zebrafish mutants revealed cardiac defects (dilated atrium, trabeculation defects, tachycardia and reduced contractility) as well as extracardiac developmental anomalies. RNA sequencing oftak1-/-mutant hearts showed downregulation of genes encoding core cardiac transcription factors, sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA-Cα is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules, including ligands of the TGFB/BMP superfamily. Consistent with these findings, CRISPR/Cas9-mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiationin vitro, while FMD-causing mutations in TAK1 reduced its ciliary localization. In conclusion, our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD, coordinated via the primary cilium.
Screening and identification of key biomarkers associated with endometriosis using bioinformatics and next generation sequencing data analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya
Published: May 2024

Endometriosis is a common cause of endometrial-type mucosa outside the uterine cavity with symptoms such as painful periods, chronic pelvic pain, pain with intercourse and infertility. However, the early diagnosis of endometriosis is still restricted. The purpose of this investigation is to identify and validate the key biomarkers of endometriosis. Next generation sequencing (NGS) dataset GSE243039 was obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between endometriosis and normal control samples were identified. After screening of DEGs, gene ontology (GO) and REACTOME pathway enrichment analyses were performed. Furthermore, a protein-protein interaction (PPI) network was constructed and modules were analysed using the Human Integrated Protein-Protein Interaction rEference (HIPIE) database and Cytoscape software, and hub genes were identified. Subsequantely, a network between miRNAs and hub genes, and network between TFss and hub genes were constructed using the miRNet and NetworkAnalyst tool, and possible key miRNAs and TFs were predicted. Finally, receiver operating characteristic curve (ROC) analysis was used to validate the hub genes. A total of 958 DEGs, including 479 up regulated genes and 479 down regulated genes, were screened between endometriosis and normal control samples. GO and REACTOME pathway enrichment analyses of the 958 DEGs showed that they were mainly involved in multicellular organismal process, developmental process, signaling by GPCR and muscle contraction. Further analysis of the PPI network and modules identified 10 hub genes, including VCAM1, SNCA, PRKCB, ADRB2, FOXQ1, MDFI, ACTBL2, PRKD1, DAPK1 and ACTC1. Possible target miRNAs, including hsa-mir-3143 and hsa-mir-2110, and target TFs, including TCF3 and CLOCK, were predicted by constructing a miRNA-hub gene regulatory network and TF-hub gene regulatory network. This investigation used bioinformatics techniques to explore the potential and novel biomarkers. These biomarkers might provide new ideas and methods for the early diagnosis, treatment, and monitoring of endometriosis.
Unlocking DOE potential selecting the most appropriate design for rAAV optimization
Authors: Tzimou Konstantina , Catalán-Tatjer David , Nielsen Lars K. , Lavado-García Jesús
Published: May 2024

The production of recombinant adeno-associated virus (rAAV) for gene therapy via triple transfection is a highly intricate process involving many cellular interactions. Each of the different elements encoded in the three required plasmids—pHelper, pRepCap, and pGOI— play a distinct role and affect different cellular pathways when producing rAAVs. The expression balance of these different elements emphasizes the critical need to fine-tune the concentration of all three plasmids and transfection reagents effectively.

The use of design of experiments (DOE) to find optimal plasmid and transfection reagent ratios is a powerful method to streamline the process. However, the choice of the DOE method and the design construction is crucial to avoid misleading results. In this work, we examined and compared four distinct DOE approaches: a rotatable central composite design (RCCD), a Box-Behnken design (BBD), a face-centered central composite design (FCCD), and a mixture design (MD). We compared the ability of the different models to predict optimal ratios, interactions among the three plasmids and transfection reagent, and the essentiality of studying the variability caused by uncontrolled random effects using blocking.

Our findings revealed that MD, when coupled with FCCD, outperformed all other tested models. This outcome underscores the importance of selecting a model that can effectively account for the biological context, ultimately yielding superior results in optimizing rAAV production.
Semaglutide interferes with postnatal growth in a diet-dependent manner
Authors: Joly Amélie , Rebiffé Lucas , Dusabyinema Yves , Dellinger Julien , Leulier François , Vadder Filipe De
Published: May 2024

Objective

Glucagon-like peptide 1 receptor agonists (GLP-1RAs) have been shown to impact glucose homeostasis and, more recently, the somatotropic axis. While the effects of GLP-1RAs have been extensively studied in the context of diet-induced obesity, their impact on physiology in other nutritional contexts have been less explored. We investigated the potential beneficial effects of the GLP-1RA semaglutide during juvenile protein malnutrition, a dietary challenge known to cause stunted growth and to disrupt metabolic homeostasis.

Methods

We used a murine model to assess the effects of twice-weekly subcutaneous injections of semaglutide during juvenile protein malnutrition. Glucose metabolism was evaluated throughin vivooral glucose tolerance test,ex vivoglucose-stimulated insulin secretion in isolated pancreatic islets and histology of the pancreas. We combined linear growth monitoring, analysis of the growth hormone/insulin-like growth factor 1 signaling pathway and liver bulk RNA sequencing to characterize the effects of semaglutide on the somatotropic axis during juvenile protein malnutrition.

Results

Semaglutide improved glucose tolerance in control and malnourished mice, but differentially impacted pancreatic islet physiology depending on the dietary protein intake. While semaglutide did not alter growth in control conditions, it further inhibited growth of malnourished mice associated with reduction in fat but not lean mass. Surprisingly, semaglutide had no discernible effect on the functionality of the somatotropic axis in malnourished mice. Liver transcriptomics revealed that semaglutide may interfere with the growth of malnourished juvenile mice by altering circadian rhythm and thermogenesis.

Conclusions

Our data reveal that semaglutide interacts differentially with the physiology of juvenile mice depending on their dietary protein intake. We found that semaglutide influences glucose metabolism and linear growth in a diet-dependent manner, underscoring the importance of examining the effects of GLP-1RAs across various nutritional contexts and developmental stages.

Highlights

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Semaglutide hampers the growth of protein-malnourished, but not control-fed, juvenile animals.

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The effects of semaglutide on linear growth are independent of alterations in the somatotropic axis.

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Semaglutide differentially alters glucose metabolism of juvenile mice depending on their dietary protein intake.
Full genome sequencing of dozens of new DNA viruses found in Spanish bat faeces
Authors: Buigues Jaime , Vinals Adria , Martinez-Recio Raquel , Monros Juan S. , Sanjuan Rafael , Cuevas Jose M.
Published: May 2024

Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 50 complete or near-complete viral genomes belonging to the families Adenoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Parvoviridae, Polyomaviridae and Smacoviridae. Of these, 28 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential.
Culture of human retinal explants as an ex vivo model for retinal gene therapy
Authors: Alsalloum Almaqdad , Khubetsova Madina , Mityaeva Olga , Volchkov Pavel
Published: May 2024

Optogenetic gene therapy may employ recombinant adeno-associated virus (AAV) vectors for specific preclinical applications in the treatment of inherited retinal diseases. Human retinal explants as an ex vivo model assist determine cellular tropism and the level of subsequent gene expression followed by delivery of viral vectors. Extracts of retinal tissue can be obtained and cultured for a certain time; thus, it is possible to transduce and confirm the effectiveness of the virus using various methods, including immunohistochemical staining. Consequently, we described method for harvesting and culturing human retinal fragments from divergent parts of the retina that differ anatomically and molecularly. The fragments were fixed, sectioned and stained. A dissociation method has also been described to obtain a retinal cell suspension that can be used in other experiments such as flow cytometry or mRNA/protein level expression assays.
Structural and biochemical characterization of LIG1 during mutagenic nick sealing of oxidatively damaged ends at the final step of DNA repair
Authors: Balu Kanal Elamparithi , Almohdar Danah , Ratcliffe Jacob , Tang Qun , Parwal Tanay , Çağlayan Melike
Published: May 2024

DNA ligase 1 (LIG1) joins broken strand-breaks in the phosphodiester backbone to finalize DNA repair pathways. We previously reported that LIG1 fails on nick repair intermediate with 3’-oxidative damage incorporated by DNA polymerase (pol) β at the downstream steps of base excision repair (BER) pathway. Here, we determined X-ray structures of LIG1/nick DNA complexes containing 3’-8oxodG and 3’-8oxorG opposite either a templating Cytosine or Adenine and demonstrated that the ligase active site engages with mutagenic repair intermediates during steps 2 and 3 of the ligation reaction referring to the formation of DNA-AMP intermediate and a final phosphodiester bond, respectively. Furthermore, we showed the mutagenic nick sealing of DNA substrates with 3’-8oxodG:A and 3’-8oxorG:A by LIG1 wild-type, immunodeficiency disease-associated variants, and DNA ligase 3α (LIG3α)in vitro. Finally, we observed that LIG1 and LIG3α seal resulting nick after an incorporation of 8oxorGTP:A by polβ and AP-Endonuclease 1 (APE1) can clean oxidatively damaged ends at the final steps. Overall, our findings uncover a mechanistic insight into how LIG1 discriminates DNA or DNA/RNA junctions including oxidative damage and a functional coordination between the downstream enzymes, polβ, APE1, and BER ligases, to process mutagenic repair intermediates to maintain repair efficiency.