bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlating Jaw Bone Growth and Nasal Morphology Among Adult Patients With Cleft Lip and Palate: A Retrospective Cephalometric Study
Authors: Chen Zhuo , Yang Jun , Mao Qirong , Shi Bing , Li Jingtao , Yin Xing
Published: April 2024

This retrospective cross-sectional study reviewed adult patients with operated cleft lip and/or palate (CL/P) and normal control, and performed comprehensive craniofacial and nasal morphological analyses based on lateral cephalometric radiographs. Pearson or Spearman correlation coefficient assessed intraclass correlation. Seven hundred fifty-seven operated patients with CL/P, and 165 noncleft normal controls were enrolled. Among the normal and CL/P groups, S-N-A angle registered positive correlations with nasal base prominence (S-N′-Sn, degrees). Upper facial height (N-ANS, mm) had positive correlations with nasal dorsum length (N′-Prn, mm) and nasal bone length (N-Na, mm). Although in patients with bilateral cleft lip and palate, there were moderate negative correlations (r=−0.541, P<0.05) with soft tissue facial profile angle (FH-N′Pog′, degree) and nasolabial angle (Cm-Sn-ULA, degree). Correlation exists between the morphology of jaw bones and external nose among patients with CL/P. Maxillary sagittal insufficiency is associated with concave nasal profile, and maxilla height is associated with nasal length.
Triangular Flap Insertion: An Option for Correction of Dog-Ears Deformity in High-Tension Areas
Authors: Song Jipeng , Jiao Hu
Published: April 2024

Dog-ear deformity is a common protrusion defect of skin tissue after the closure of a surgical wound, affecting patients’ appearance and quality of life. The common methods for correcting dog ears involve the removal of excess tissue in different directions or shapes after extending the incision along the long axis of the original wound. However, the literature regarding tissue preservation techniques for dog-ear correction is poor, especially for areas with insufficient skin tissue or high tension. The authors modified the original design of direct excisions, which transferred excess tissue from the horizontal axis of the wound to the longitudinal axis, thereby absorbing longitudinal tension and relieving linear scar contracture. This technique provides a way to correct dog ears without removing excess healthy tissue, especially as an option for dog-ear correction in high-tension areas.
miR-208a-3p regulated by circUQCRC2 suppresses ischemia/reperfusion-induced acute kidney injury by inhibiting CELF2-mediated tubular epithelial cell apoptosis, inflammation and ferroptosis
Authors: Huang Peng , Meng Lingzhang , Pang Jun , Huang Haiting , Ma Jing , He Linlin , Lin Xu
Published: April 2024

Background: Acute kidney injury (AKI) is a prevalent clinical syndrome with persistent kidney dysfunction. Renal ischemia/reperfusion (I/R) injury is a major cause of AKI. miR-208a-3p overexpression attenuated myocardial I/R injury. This study aims to investigate the role and mechanism of miR-208a-3p in I/R-induced AKI. Methods: AKI models were established using hypoxia/reoxygenation (H/R)-exposed tubule epithelial cell HK-2 and I/R-induced mice. The function and mechanism of miR-208a-3p were investigated by gain- or loss-of-function methods using real-time PCR, CCK-8, flow cytometry, ELISA, western blot, hematoxylin-eosin staining, terminal deoxynucleotidyl transferase dUTP nick end labeling assay, detection of Fe2+, reactive oxygen species, blood urea nitrogen and creatinine, and luciferase reporter assay. Results: miR-208a-3p expression was suppressed, while the expression of CELF2 and circular RNA ubiquinol-cytochrome c reductase core protein 2 (circUQCRC2) was increased in both AKI models. miR-208a-3p upregulation or circUQCRC2 silencing increased the viability, decreased the levels of proinflammatory cytokines (TNF-α, IL-1β, and IL-6), reduced apoptosis and contents of Fe2+ and reactive oxygen species, elevated expression of GPX4 and SLC7A11, and reduced ACSL4 expression in H/R-stimulated HK-2 cells. In addition, miR-208a-3p improved kidney function by alleviating renal injury, apoptosis, inflammation, and ferroptosis in AKI mouse model. CELF2 was a target gene of miR-208a-3p, which was negatively modulated by circUQCRC2. Overexpression of CELF2 blocked the function of miR-208a-3p upregulation or circUQCRC2 silencing on H/R-treated HK-2 cells. Moreover, the effects of circUQCRC2 downregulation on H/R-injured cells were also reversed by miR-208a-3p inhibitor. Conclusions: miR-208a-3p regulated by circUQCRC2 could attenuate I/R-induced AKI by inhibiting CELF2-mediated tubular epithelial cell apoptosis, inflammation and ferroptosis. This study provides potential therapeutic targets for I/R-induced AKI.
VENOARTERIAL EXTRACORPOREAL MEMBRANE OXYGENATION REDUCES MYOCARDIAL AND MITOCHONDRIAL DAMAGE IN ACUTE MYOCARDIAL INFARCTION
Authors: Ni Ming , Dong Aiqiang , Zhu Xian , Li Xuebiao , Xu Guocong , Gao Ning , Wei Dongdong , Wang Yifan , Kong Minjian
Published: April 2024

Background: Myocardial infarction (MI) is a common cardiovascular disease with a high fatality rate once accompanied by cardiogenic shock. The efficacy of extracorporeal membrane oxygenation (ECMO) in treating MI is controversial. Methods: MI was induced by ligating the left anterior descending artery (LAD) in adult male rats. Groups were defined as follows: MI group, reperfusion for 90 min after 30 min of LAD occlusion; MI + ECMO group, reperfusion and ECMO were performed for 90 min immediately after 30 min of LAD occlusion; prolonged MI + ECMO group, ECMO was used immediately after 30 min of occlusion with persistent occlusion of the LAD for an additional 30 min, followed by 90 min of reperfusion. The myocardial infarct size and mitochondrial morphology and function data were collected and compared of each group. Results: The ECMO groups had a smaller myocardial infarct size and larger percentage ejection fraction. Compared with the prolonged MI + ECMO group, the immediate reperfusion group had a lower percentage of infarct size (63.28% vs. 17.97% vs. 31.22%, MI vs. MI + ECMO vs. prolonged MI + ECMO). Mitochondria isolated from the ischemic zone showed an intact mitochondrial structure, including fewer voids and broken cristae, and preserved activity of mitochondrial complex II and complex IV in ECMO groups. Conclusions: ECMO support in MI can reduce myocardial injury despite delayed coronary reperfusion.
Health care providers’ communication with pediatric patients and carers: a best practice implementation project
Authors: Shoaran Maryam , Hajebrahimi Sakineh , Kabiri Neda , Salehi Pourmehr Hanieh , Talebpour Amin
Published: April 2024

Introduction and objectives:

Health care providers need a high level of communication skills in dealing with pediatric patients and their carers. The objective of this project was to evaluate current practice and implement best practices promoting health care provider communication with pediatric patients and carers in a children's hospital in Tabriz, Iran.

Methods:

This project used the JBI Model of Evidence-Based Healthcare, which guided the conceptualization of evidence implementation, context analysis, project implementation, and evaluation of outcomes using evidence-based quality indicators. An audit and feedback strategy was adopted to measure baseline compliance with best practices, develop strategies to address areas of non-compliance, and conduct a final audit to measure any changes in compliance. Four criteria were developed for the baseline and follow-up audits. Criteria 1 and 2 were evaluated using a sample of 30 health care providers, while Criteria 3 and 4 were evaluated using a sample of 80 pediatric patients and carers.

Results:

All four criteria improved at the end of the project. Criterion 1 (health care staff receive communication skills training) had the highest mean score at baseline and follow-up (63% and 83%, respectively). Criterion 2 (implementation of local strategies by health care organizations) increased from 45% to 55%. However, this rate of improvement was the lowest of all the criteria. Criterion 3 (pediatric patients receive relevant education) improved from low to moderate, rising from 18% to 49%. A more significant improvement was noted for Criterion 4 (parents receive relevant education), which rose from 19% to 56%.

Conclusions:

The strategies implemented in this project successfully improved health care provider communication with pediatric patients and their carers. To ensure project sustainability, repeat audits will be conducted after 3, 6, and 12 months.

Spanish abstract:

http://links.lww.com/IJEBH/A199
Rhein kills Actinobacillus pleuropneumoniae, reduces biofilm formation, and effectively treats bacterial lung infections in mice
Authors: Ding Haifeng , Bai Yilin , Luo Weiyu , Li Hao , Zhu Chunling , Zhao Xueqin , Sun Huarun , Wen Yuliang , Zhang Wei , Zhang Shouping , Wen Bo , Wang Ruibiao , Zhang Longfei , Liu Xuehan , Shen Jiyuan , Hu Jianhe , Wang Lei , Bai Yueyu , Liao Chengshui , Wu Yundi , Wu Xilong , Ding Ke
Published: April 2024

Background.
Actinobacillus pleuropneumoniae, a member of the Pasteurellaceae family, is known for its highly infectious nature and is the primary causative agent of infectious pleuropneumonia in pigs. This disease poses a considerable threat to the global pig industry and leads to substantial economic losses due to reduced productivity, increased mortality rates, and the need for extensive veterinary care and treatment. Due to the emergence of multi-drug-resistant strains, Chinese herbal medicine is considered one of the best alternatives to antibiotics due to its unique mechanism of action and other properties. As a type of Chinese herbal medicine, Rhein has the advantages of a wide antibacterial spectrum and is less likely to develop drug resistance, which can perfectly solve the limitations of current antibacterial treatments.

Methods. The killing effect of Rhein on A. pleuropneumoniae was detected by fluorescence quantification of differential expression changes of key genes, and scanning electron microscopy was used to observe the changes in A. pleuropneumoniae status after Rhein treatment. Establishing a mouse model to observe the treatment of Rhein after A. pleuropneumoniae infection.

Results. Here, in this study, we found that Rhein had a good killing effect on A. pleuropneumoniae and that the MIC was 25 µg ml−1. After 3 h of action, Rhein (4×MIC) completely kills A. pleuropneumoniae and Rhein has good stability. In addition, the treatment with Rhein (1×MIC) significantly reduced the formation of bacterial biofilms. Therapeutic evaluation in a murine model showed that Rhein protects mice from A. pleuropneumoniae and relieves lung inflammation. Quantitative RT-PCR (Quantitative reverse transcription polymerase chain reaction is a molecular biology technique that combines both reverse transcription and polymerase chain reaction methods to quantitatively detect the amount of a specific RNA molecule) results showed that Rhein treatment significantly downregulated the expression of the IL-18 (Interleukin refers to a class of cytokines produced by white blood cells), TNF-α, p65 and p38 genes. Along with the downregulation of genes such as IL-18, it means that Rhein has an inhibitory effect on the expression of these genes, thereby reducing the activation of inflammatory cells and the production of inflammatory mediators. This helps reduce inflammation and protects tissue from further damage.

Conclusions. This study reports the activity of Rhein against A. pleuropneumoniae and its mechanism, and reveals the ability of Rhein to treat A. pleuropneumoniae infection in mice, laying the foundation for the development of new drugs for bacterial infections.
Relationship Between Therapeutic Activity and Preferential Targeting of Toxic Soluble Aggregates by Amyloid-Beta-Directed Antibodies
Authors: Kaplan Johanne M. , Gibbs Ebrima , Coutts Juliane , Zhao Beibei , Mackenzie Ian , Cashman Neil R.
Published: April 2024

Background

Amyloid-beta (Aβ)-directed antibodies tested clinically for therapeutic activity against Alzheimer’s disease (AD) have shown varying degrees of efficacy. Although all of these antibodies target the Aβ peptide, their binding profile to different molecular species of Aβ differs and may underlie the observed variability in clinical outcomes.

Objective

Explore the relationship between targeting of soluble toxic Aβ species and therapeutic efficacy.

Methods

Surface plasmon resonance (SPR) was used to conduct a side-by-side comparison of the binding of various Aβ-directed antibodies to monomers and soluble Aβ oligomers from AD brains. Immunohistochemistry was performed to assess reactivity with plaque. Preclinical activity was assessed in human amyloid precursor protein (APP) transgenic mouse models of AD.

Results

Non-selective, pan-Aβ reactive antibodies such as crenezumab and gantenerumab, which have failed to produce a clinical benefit, bound all forms of Aβ tested. In a competition assay, these antibodies lost the ability to bind toxic AD brain oligomers when exposed to monomers. Aggregate-selective antibodies such as aducanumab, lecanemab and donanemab, showed reduced monomer binding and a greater ability to withstand monomer competition which correlated with their reported inhibition of cognitive decline. Of the antibodies in earlier stages of clinical testing, ACU193 and PMN310 displayed the greatest ability to retain binding to toxic AD brain oligomers while PRX h2731 was highly susceptible to monomer competition. Plaque binding was observed with all aggregate-reactive antibodies with the exception of PMN310, which was strictly selective for soluble oligomers. Targeting of oligomers by PMN310 protected cognition and was not associated with microhemorrhages in mouse models of AD.

Conclusions

Overall, these results suggest that selectivity for soluble toxic Aβ oligomers may be a driver of clinical efficacy, with a potentially reduced risk of ARIA if engagement with plaque is minimized.
Exploring automated Feature Selection for Model-based and Density-based clustering with application to NCI 60 data
Authors: Ahuja Suruchi Jai Kumar
Published: April 2024

A major objective of clustering is to identify groups in the data that maximizes the similarity between objects within the same cluster and minimizes the similarity between different clusters. A challenge for data clustering, and unsupervised learning in general, is that there is often no mechanism for feature selection. In contrast, supervised learning problems can be solved in connection with feature selection methods, such as subset selection or LASSO like penalties. However, variable selection in unsupervised learning problems is not well defined since there is no response variable, which makes subset selection is far more challenging.

Consequently, there have been comparatively few methods that automate feature selection for clustering. Typically, when faced with high dimensionality, or the possibility of irrelevant features, an investigator will employ dimension reduction techniques with standard clustering algorithms. In this work, I examine two methods that encode feature selection into the clustering process, cluster variable selection via model-based clustering and density-based clustering, using the Clustvarsel and DBSCAN packages in the R programming language. These methods were applied to the NCI-60 data and compared to the Principal Component based k-means over different parameter settings. Results indicate major advantages in the performance of PC based k-means when compared to feature selection via Clustvarsel and DBSCAN, and major limitations in Clustvarsel.
"Toki", a light low-cost video system for seabed research: performance and precision of Tehuelche scallop (Aequipecten tehuelchus) survey estimates in San José Gulf, Argentina
Authors: Trobbiani Gastón Andrés , Getino Mamet Leandro N , Irigoyen Alejo J , Parma Ana M
Published: April 2024

Studies of benthic abundance and biodiversity are essential for fisheries management and environmental impact assessments. In the case of commercial species, such as Tehuelche scallop (Aequipecten tehuelchus), accurate information on the stocks and their densities is crucial. The standard survey method used to estimate abundance of Tehuelche scallops in San José Gulf, Argentina Patagonia, based on visual counts obtained by divers is labor-intensive and limited to diving depths. This study introduces a light low-cost video remote system, named "Toki", for monitoring scallop beds from small boats. Toki consists of a steel pyramidal structure that houses two cameras, capable of capturing georeferenced high-definition images. The performance of Toki for estimating the density and size composition of scallops was evaluated. The results demonstrate that Toki provides efficient and accurate density estimates, with variations that can be attributed to observer experience and environmental factors such as bottom algal cover. The size frequency distributions obtained from Toki aligned well with those from hand collection, which allows such measurement for beds beyond diveable depths. Toki offers advantages in terms of spatial coverage and permanent data records. While there are some limitations, such as processing time for image analysis, future developments based on artificial intelligence can overcome these challenges. Toki has the potential to improve the monitoring of scallop beds and data collection.
Crystal structure of a bacterial photoactivated adenylate cyclase determined at room temperature by serial femtosecond crystallography
Authors: Kapetanaki Sofia M. , Coquelle Nicolas , von Stetten David , Byrdin Martin , Rios-Santacruz Ronald , Bean Richard , Bielecki Johan , Boudjelida Mohamed , Fekete Zsuzsana , Grime Geoffrey W. , Han Huijong , Hatton Caitlin , Kantamneni Sravya , Kharitonov Konstantin , Kim Chan , Kloos Marco , Koua Faisal H.M. , de Diego Martinez Iñaki , Melo Diogo , Rane Lukas , Round Adam , Round Ekaterina , Sarma Abhisakh , Schubert Robin , Schulz Joachim , Sikorski Marcin , Vakili Mohammad , Valerio Joana , Vitas Jovana , de Wijn Raphael , Wrona Agnieszka , Zala Ninon , Pearson Arwen , Dörner Katerina , Schirò Giorgio , Garman Elspeth F. , Lukács András , Weik Martin
Published: April 2024

OaPAC is a recently discoveredblue-lightusing flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacteriumOscillatoria acuminatathat uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report the crystal structures of the enzyme in the absence of its natural substrate determined from room temperature serial crystallography data collected at both an X-ray free electron laser and a synchrotron and we compare them with the cryo macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6 mutation in the blue-light using flavin adenosine dinucleotide domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side-chain of the critical Q48 residue. These studies pave the way for ps - ms time-resolved serial crystallography experiments at X-ray free electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well-studied ps - ms spectroscopic intermediates.

Synopsis

Structures of the dark-adapted state of a photoactivated adenylate cyclase are determined from serial crystallography (SX) data collected at room temperature at an X-ray free electron laser (XFEL) and a synchrotron and are compared with cryo macromolecular crystallography (MX) synchrotron structures obtained by us and others. These structures of the wild-type enzyme in combination with the cryo MX synchrotron structure of a light-sensor domain mutant provide insight into the hydrogen bond network rearrangement upon blue-light illumination and pave the way for the determination of structural intermediates of the enzyme by time-resolved SX.
Innate liking and disgust reactions elicited by intraoral capsaicin in male mice
Authors: Han Yibin , Tanaka Daisuke H. , Uesaka Naofumi
Published: April 2024

Liking and disgust are the primary positive and negative emotions, respectively, and are crucial for nutrient intake and toxin avoidance. These emotions are induced by multimodal stimuli such as taste, olfactory, and somatosensory inputs, and their dysregulation is evident in various psychiatric disorders. To understand the biological basis of liking and disgust, it is crucial to establish an animal model that allows for quantitative estimation of liking and disgust in response to multimodal stimuli. The only readout shared by many species, including humans, for liking and disgust, has been taste reactivity. However, readouts of non-taste stimuli-induced emotions remain unestablished. Here, we show that intraoral administration of capsaicin, a chemosomatosensory stimulus, elicits orofacial and bodily reactions in male mice similar to those observed in taste reactivity. Capsaicin induced liking reactions at low concentrations and disgust reactions at high concentrations. Capsaicin-induced disgust reactions consisted of various reactions, including gape and forelimb flail, with the proportion of each reaction among the disgust reactions being similar to that induced by bitter and sour stimuli. These findings indicate that orofacial and bodily reactions, defined as taste reactivity, are elicited not only by taste stimuli, but also by intraoral chemosomatosensory stimuli. Understanding the biological basis of capsaicin-induced orofacial and bodily reactions will advance our understanding of the fundamental mechanisms underlying liking and disgust across sensory modalities.
Tissue and cellular spatiotemporal dynamics in colon aging
Authors: Daly Aidan C. , Cambuli Francesco , Äijö Tarmo , Lötstedt Britta , Marjanovic Nemanja , Kuksenko Olena , Smith-Erb Matthew , Fernandez Sara , Domovic Daniel , Van Wittenberghe Nicholas , Drokhlyansky Eugene , Griffin Gabriel K , Phatnani Hemali , Bonneau Richard , Regev Aviv , Vickovic Sanja
Published: April 2024

Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ∼1,500 mouse gut tissues profiled by spatial transcriptomics and ∼400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.
Lipoxin A4/FPR2 signaling mitigates ferroptosis of alveolar epithelial cells via NRF2-dependent pathway during lung ischemia-reperfusion injury
Authors: Kollareth Denny Joseph Manual , Leroy Victoria , Tu Zhenxiao , Woolet-Stockton Makena Jade , Kamat Manasi , Garrett Timothy J. , Atkinson Carl , Cai Guoshuai , Upchurch Gilbert R. , Sharma Ashish K.
Published: April 2024

BACKGROUND

Post-lung transplantation (LTx) injury can involve sterile inflammation due to ischemia-reperfusion injury (IRI). We investigated the cell-specific role of ferroptosis (excessive iron-mediated cell death) in mediating lung IRI and determined if specialized pro-resolving mediators such as Lipoxin A4 (LxA4) can protect against ferroptosis in lung IRI.

METHODS

Single-cell RNA sequencing of lung tissue from post-LTx patients was analyzed. Lung IRI was evaluated in C57BL/6 (WT), formyl peptide receptor 2 knockout (Fpr2−/−) and nuclear factor erythroid 2-related factor 2 knockout (Nrf2−/−) mice using a hilar-ligation model with or without LxA4administration. Furthermore, the protective efficacy of LxA4was evaluated employing a murine orthotopic LTx model andin vitrostudies using alveolar type II epithelial (ATII) cells.

RESULTS

Differential expression of ferroptosis-related genes was observed in post-LTx patient samples compared to healthy controls. A significant increase in the levels of oxidized lipids and reduction in the levels of intact lipids were observed in mice subjected to IRI compared to shams. Furthermore, pharmacological inhibition of ferroptosis with liproxstatin-1 mitigated lung IRI and lung dysfunction. Importantly, LxA4treatment attenuated pulmonary dysfunction, ferroptosis and inflammation in WT mice subjected to lung IRI, but not inFpr2−/−orNrf2−/−mice, after IRI. In the murine LTx model, LxA4treatment increased PaO2levels and attenuated lung IRI. Mechanistically, LxA4-mediated protection involves increase in NRF2 activation and glutathione concentration as well as decrease in MDA levels in ATII cells.

CONCLUSIONS

LxA4/FPR2 signaling on ATII cells mitigates ferroptosis via NRF2 activation and protects against lung IRI.
Modeling tumors as species-rich ecological communities
Authors: Aguadé-Gorgorió Guim , Anderson Alexander R.A. , Solé Ricard
Published: April 2024

Many advanced cancers resist therapeutic intervention. This process is fundamentally related to intra-tumor heterogeneity: multiple cell populations, each with different mutational and phenotypic signatures, coexist within a tumor and its metastatic nodes. Like species in an ecosystem, many cancer cell populations are intertwined in a complex network of ecological interactions. Most mathematical models of tumor ecology, however, cannot account for such phenotypic diversity nor are able to predict its consequences. Here we propose that the Generalized Lotka-Volterra model (GLV), a standard tool to describe complex, species-rich ecological communities, provides a suitable framework to describe the ecology of heterogeneous tumors. We develop a GLV model of tumor growth and discuss how its emerging properties, such as outgrowth and multistability, provide a new understanding of the disease. Additionally, we discuss potential extensions of the model and their application to three active areas of cancer research, namely phenotypic plasticity, the cancer-immune interplay and the resistance of metastatic tumors to treatment. Our work outlines a set of questions and a tentative road map for further research in cancer ecology.
Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina
Authors: Zapp Sören J. , Khani Mohammad H. , Schreyer Helene M. , Sridhar Shashwat , Ramakrishna Varsha , Krüppel Steffen , Mietsch Matthias , Protti Dario A. , Karamanlis Dimokratis , Gollisch Tim
Published: April 2024

A standard circuit motif in sensory systems is the pooling of sensory information from an upstream neuronal layer. A downstream neuron thereby collects signals across different locations in stimulus space, which together compose the neuron’s receptive field. In addition, nonlinear transformations in the signal transfer between the layers give rise to functional subunits inside the receptive field. For ganglion cells in the vertebrate retina, for example, receptive field subunits are thought to correspond to presynaptic bipolar cells. Identifying the number and locations of subunits from the stimulus–response relationship of a recorded ganglion cell has been an ongoing challenge in order to characterize the retina’s functional circuitry and to build computational models that capture nonlinear signal pooling. Here we present a novel version of spike-triggered non-negative matrix factorization (STNMF), which can extract localized subunits in ganglion-cell receptive fields from recorded spiking responses under spatiotemporal white-noise stimulation. The method provides a more than 100-fold speed increase compared to a previous implementation, which can be harnessed for systematic screening of hyperparameters, such as sparsity regularization. We demonstrate the power and flexibility of this approach by analyzing populations of ganglion cells from salamander and primate retina. We find that subunits of midget as well as parasol ganglion cells in the marmoset retina form separate mosaics that tile visual space. Moreover, subunit mosaics show alignment with each other for ON and OFF midget as well as for ON and OFF parasol cells, indicating a spatial coordination of ON and OFF signals at the bipolar-cell level. Thus, STNMF can reveal organizational principles of signal transmission between successive neural layers, which are not easily accessible by other means.
Impact of phylogeny on the inference of functional sectors from protein sequence data
Authors: Dietler Nicola , Abbara Alia , Choudhury Subham , Bitbol Anne-Florence
Published: April 2024

Statistical analysis of multiple sequence alignments of homologous proteins has revealed groups of coevolving amino acids called sectors. These groups of amino-acid sites feature collective correlations in their amino-acid usage, and they are associated to functional properties. Modeling showed that nonlinear selection on an additive functional trait of a protein is generically expected to give rise to a functional sector. These modeling results motivated a principled method, called ICOD, which is designed to identify functional sectors, as well as mutational effects, from sequence data. However, a challenge for all methods aiming to identify sectors from multiple sequence alignments is that correlations in amino-acid usage can also arise from the mere fact that homologous sequences share common ancestry, i.e. from phylogeny. Here, we generate controlled synthetic data from a minimal model comprising both phylogeny and functional sectors. We use this data to dissect the impact of phylogeny on sector identification and on mutational effect inference by different methods. We find that ICOD is most robust to phylogeny, but that conservation is also quite robust. Next, we consider natural multiple sequence alignments of protein families for which deep mutational scan experimental data is available. We show that in this natural data, conservation and ICOD best identify sites with strong functional roles, in agreement with our results on synthetic data. Importantly, these two methods have different premises, since they respectively focus on conservation and on correlations. Thus, their joint use can reveal complementary information.

Author Summary

Proteins perform crucial functions in the cell. The biological function of a protein is encoded in its amino-acid sequence. Natural selection acts at the level of function, while mutations arise randomly on sequences. In alignments of sequences of homologous proteins, which share common ancestry and common function, the amino acid usages at different sites can be correlated due to functional constraints. In particular, groups of collectively correlated amino acids, termed sectors, tend to emerge due to selection on functional traits. However, correlations can also arise from the shared evolutionary history of homologous proteins, even without functional constraints. This may obscure the inference of functional sectors. By analyzing controlled synthetic data as well as natural protein sequence data, we show that two very different methods allow to identify sectors and mutational effects in a way that is most robust to phylogeny. We suggest that considering both of these methods allows a better identification of functionally important sites from protein sequences. These results have potential impact on the design of new functional sequences.
demuxSNP: supervised demultiplexing scRNAseq using cell hashing and SNPs
Authors: Lynch Michael P. , Wang Yufei , Gatto Laurent , Culhane Aedin C.
Published: April 2024

Background

Multiplexing single-cell RNA sequencing experiments reduces sequencing cost and facilitates larger scale studies. However, factors such as cell hashing quality and class size imbalance impact demultiplexing algorithm performance, reducing cost effectiveness

Findings

We propose a supervised algorithm, demuxSNP, leveraging both cell hashing and genetic variation between individuals (SNPs). The supervised algorithm addresses fundamental limitations in demultiplexing with only one data modality. The genetic variants (SNPs) of the subset of cells assigned with high confidence using a probabilistic hashing algorithm are used to train a KNN classifier that predicts the demultiplexing classes of unassigned or uncertain cells. We benchmark demuxSNP against hashing (HTODemux, cellhashR, GMM-demux, demuxmix) and genotype-free SNP (souporcell) methods on simulated and real data from renal cell cancer. Our results demonstrate that demuxSNP outperformed standalone hashing methods on low quality hashing data, improving overall classification accuracy and allowing more high RNA quality cells to be recovered. Through varying simulated doublet rates, we show genotype-free SNP methods are unable to identify biological samples with low cell counts at high doublet rates. When compared to unsupervised SNP demultiplexing methods, demuxSNP’s supervised approach was more robust to doublet rate in experiments with class size imbalance.

Conclusions

demuxSNP is a performant demultiplexing approach that uses hashing and SNP data to demultiplex datasets with low hashing quality where biological samples are genetically distinct. Unassigned cells (negatives) with high RNA quality can be recovered, making more cells available for analysis, especially when applied to data with low hashing quality or suspected misassigned cells. Pipelines for simulated data and processed benchmarking data for 5-50% doublets are publicly available. demuxSNP is available as an R/Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.demuxSNP).
Reinforcement learning enhances training and performance in skilled alpine skiers compared to traditional coaching instruction
Authors: Magelssen Christian , Gilgien Matthias , Tajet Simen Leithe , Losnegard Thomas , Haugen Per , Reid Robert , Frömer Romy
Published: April 2024

Skilled athletes need powerful movement strategies to solve tasks effectively. Typically, athletes learn these strategies with instruction-based teaching methods where coaches offer athletes a correct solution. Inspired by recent evidence from decision neuroscience, we asked whether skilled athletes learn strategy choices better with an evaluation-based training strategy (reinforcement learning). To address this question, we conducted a three-day learning experiment with skilled alpine ski racers (n=98) designed to improve their performance on flat slopes on slalom with four strategies at their disposal to achieve this goal. We compared performance and strategy choices of three groups: a reinforcement learning group, that only received feedback about their race times after every run, a supervised (free choice) learning group, that received strategy instructions from their coach, and a supervised (target skill) learning group, being coached to use the theoretically optimal strategy for skiing well on flats. We found that despite making similar strategy choices, the skiers in the reinforcement learning group, showed greater improvements in their race times during the training sessions than their counterparts in the supervised (free choice) learning group and outperformed them during a subsequent retention test. Surprisingly, the skiers in the reinforcement learning group even showed descriptively (but not significantly) better performance than those in the supervised (target skill) learning group. Our findings show that reinforcement learning can be an effective training strategy for improving strategy choices and performance among skilled athletes, even among the best ones.
Gestational exposure to high heat-humidity conditions impairs mouse embryonic development
Authors: Manhas Avinchal , Sarkar Amritesh , GAYEN SRIMONTA
Published: April 2024

Unprecedented rates of global warming have created an existential challenge for the sustainable survival of species on this planet. Tropical conditions of high ambient temperature and relative humidity are extremely vulnerable to maternal-child health. Emerging epidemiological studies depict that exposure to extremely hot weather conditions during pregnancy leads to an array of adverse pregnancy outcomes, such as low birth weight, stillbirth, preterm delivery, congenital abnormalities and adult-onset disorders. A lack of understanding of the underlying molecular pathophysiology limits us from developing an effective combat strategy in terms of targeted therapeutics to improvise the combined teratogenic effects of high heat-humidity in pregnancy. To address this, it is important to delineate the effect of hot-humid weather conditions on the process of embryogenesis. However, working with human embryos is technically and ethically challenging. In this study, we have established a mouse model of heat-humidity stress during pregnancy, which essentially recapitulates the adverse pregnancy outcomes observed in humans. Importantly, we have profiled the impact of high heat-humidity exposure during gestation at different stages of embryogenesis using this mouse model. Our results indicate that the teratogenicity of heat-humidity stress gets manifested in a cumulative manner, starting from the pre-implantation stage and becomes severe at the mid-gestation, culminating in significantly higher embryonic deaths and malformations at the late gestational stage of mouse embryogenesis. Overall, our study paves the path for exploring the underlying molecular players that get dysregulated under gestational exposure to hot and humid conditions, resulting in severe embryonic defects.
mini-Complexome Profiling (mCP), an FDR-controlled workflow for global targeted detection of protein complexes
Authors: Amedei Hugo , Paul Niels , Foo Brian , Neuenroth Lisa , Lehnart Stephan E. , Urlaub Henning , Lenz Christof
Published: April 2024

Introduction

Co-fractionation mass spectrometry couples native-like separations of protein/protein complexes with mass spectrometric proteome analysis for global characterization of protein networks. The technique allows for both de novo detection of complexes and for the detection of subtle changes in their protein composition. The typical requirement for fine-grained fractionation of >80 fractions, however, translates into significant demands on sample quantity and mass spectrometric instrument time, and represents a significant barrier to experimental replication and the use of scarce sample material (ex. Patient biopsies).

Methods

We developed mini-Complexome Profiling (mCP), a streamlined workflow with reduced requirements for fractionation and, thus, biological material and laboratory and instrument time. Soluble and membrane-associated protein complexes are extracted from biological material under mild conditions, and fractionated by Blue Native electrophoresis using commercial equipment. Each fraction is analyzed by data independent acquisition mass-spectrometry, and known protein complexes are detected based on the coelution of known components using a novel R package with a controlled false discovery rate approach. The tool is available to the community on a GitHub repository.

Results

mCP was benchmarked using HEK293 cell lysate and exhibited performance similar to established workflows, but from a significantly reduced number of fractions. We then challenged mCP by performing comparative complexome analysis of cardiomyocytes isolated from different chambers from a single mouse heart, where we identified subtle chamber-specific changes in mitochondrial OxPhos complexes.

Discussion

The reduced sample and instrument time requirements open up new applications of co-fractionation mass spectrometry, specifically for the analysis of sparse samples such as human patient biopsies. The ability to identify subtle changes between similar tissue types (left/right ventricular and atrial cardiomyocytes) serves as a proof of principle for comparative analysis of mild/asymptomatic disease states.
Biases in ARG-based inference of historical population size in populations experiencing selection
Authors: Marsh Jacob I. , Johri Parul
Published: April 2024

Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ARG-based approaches to demographic inference in typical empirical analyses are susceptible to mis-inference due to these effects. To address this, we developed highly realistic forward simulations of human andDrosophila melanogasterpopulations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, though it could cause mis-inference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference ofD. melanogasterpopulations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid mis-inference due to the linked effects of selection.
Assessing drug uptake and response differences in 2D and 3D cellular environments using stimulated Raman scattering microscopy
Authors: Xu Fiona Xi , Sun Rui , Owens Ryan , Hu Kailun , Fu Dan
Published: April 2024

The architecture of cell culture—two-dimensional (2D) versus three-dimensional (3D)—significantly impacts various cellular factors, including cell-cell interactions, nutrient and oxygen gradients, metabolic activity, and gene expression profiles. This can result in different cellular responses during cancer drug treatment, with 3D-cultured cells often exhibiting higher resistance to chemotherapeutic drugs. While various genetic and proteomic analyses have been employed to investigate the underlying mechanisms of this increased resistance, complementary techniques that provide experimental evidence of spatial molecular profiling data are limited. Stimulated Raman scattering (SRS) microscopy has demonstrated its capability to measure both intracellular drug uptake and growth inhibition. In this work, we applied three-band SRS imaging to 2D and 3D cell cultures and provided a comparative analysis of drug uptake and response with the goal of understanding whether the difference in drug uptake explains the drug resistance in 3D culture compared to 2D. Our investigations revealed that despite similar intracellular drug levels in 2D and 3D A549 cells during lapatinib treatment, the growth of 3D spheroids is less impacted, supporting an enhanced drug tolerance in the 3D microenvironment. We further elucidated drug penetration patterns and the resulting heterogeneous cellular responses across different spheroid layers. Additionally, we investigated the role of the extracellular matrix in modulating drug delivery and cell response, and we discovered that limited drug penetration in 3D could also contribute to lower drug response. Our study provides valuable insights into the intricate mechanisms of increased drug resistance in 3D tumor models during cancer drug treatments.
Therapeutic Activity of Resolvin D1 (RvD1) in Murine MASH
Authors: Navarro-Corcuera Amaia , Zhu Yiwei , Ma Fanglin , Gupta Neha , Asplund Haley , Yuan Feifei , Friedman Scott , Sansbury Brian E. , Huang Xin , Cai Bishuang
Published: April 2024

Background and Aims

Recent studies have highlighted the beneficial effect of resolvin D1 (RvD1), a DHA-derived specialized pro-resolving mediator, on metabolic dysfunction-associated steatohepatitis (MASH), but the underlying mechanisms are not well understood. Our study aims to determine the mechanism by which RvD1 protects against MASH progression.

Methods

RvD1 was administered to mice with experimental MASH, followed by bulk and single-cell RNA sequencing analysis. Primary cells including bone marrow–derived macrophages (BMDMs), Kupffer cells, T cells, and primary hepatocytes were isolated to elucidate the effect of RvD1 on inflammation, cell death, and fibrosis regression genes.

Results

Hepatic tissue levels of RvD1 were decreased in murine and human MASH, likely due to an expansion of pro-inflammatory M1-like macrophages with diminished ability to produce RvD1. Administering RvD1 reduced inflammation, cell death, and liver fibrosis. Mechanistically, RvD1 reduced inflammation by suppressing the Stat1-Cxcl10 signaling pathway in macrophages and prevented hepatocyte death by alleviating ER stress-mediated apoptosis. Moreover, RvD1 inducedMmp2and decreasedActa2expression in hepatic stellate cells (HSCs), and promotedMmp9andMmp12expression in macrophages, leading to fibrosis regression in MASH.

Conclusions

RvD1 reduces Stat1-mediated inflammation, mitigates ER stress-induced apoptosis, and promotes MMP-mediated fibrosis regression in MASH. This study highlights the therapeutic potential of RvD1 to treat MASH.

Impact and implications

Metabolic dysfunction–associated steatohepatitis (MASH) is an increasing healthcare burden worldwide. Current treatments for MASH and its sequelae are very limited. Recent studies highlighted the therapeutic benefit of specialized pro-resolving mediators (SPMs), including resolvin D1 (RvD1), in liver diseases. However, the mechanisms underlying these beneficial effects are not well understood. Based on unbiased transcriptomic analyses using bulk and single-cell RNA sequencing in RvD1-treated MASH livers, we show that RvD1 suppresses Stat1-mediated inflammatory responses and ER stress-induced apoptosis, and induces gene expression related to fibrosis regression. Our study provides new mechanistic insight into the role of RvD1 in MASH and highlights its therapeutic potential to treat MASH.

Highlights

Liver RvD1 levels are decreased in MASH patients and MASH mice

RvD1 administration suppresses Stat1-mediated inflammatory response

RvD1 administration alleviates ER stress-induced apoptosis

RvD1 administration induces fibrosis regression gene expression