bluuebunny/crossref_metadata_2025 huggingface dataset:
PyF2F: a robust and simplified fluorophore-to-fluorophore distance measurement tool for Protein interactions from Imaging Complexes after Translocation experiments
Authors: Hernandez Altair C , Ortiz Sebastian , Betancur Laura I , Dojčilović Radovan , Picco Andrea , Kaksonen Marko , Oliva Baldo , Gallego Oriol
Published: March 2024

Structural knowledge of protein assemblies in their physiological environment is paramount to understand cellular functions at the molecular level. Protein interactions from Imaging Complexes after Translocation (PICT) is a live-cell imaging technique for the structural characterization of macromolecular assemblies in living cells. PICT relies on the measurement of the separation between labelled molecules using fluorescence microscopy and cell engineering. Unfortunately, the required computational tools to extract molecular distances involve a variety of sophisticated software programs that challenge reproducibility and limit their implementation to highly specialized researchers. Here we introduce PyF2F, a Python-based software that provides a workflow for measuring molecular distances from PICT data, with minimal user programming expertise. We used a published dataset to validate PyF2F’s performance.
Pain in the Context of Sensory Deafferentation
Authors: Cohen Steven P. , Caterina Michael J. , Yang Su-Yin , Socolovsky Mariano , Sommer Claudia
Published: March 2024

Pain that accompanies deafferentation is one of the most mysterious and misunderstood medical conditions. Prevalence rates for the assorted conditions vary considerably but the most reliable estimates are greater than 50% for strokes involving the somatosensory system, brachial plexus avulsions, spinal cord injury, and limb amputation, with controversy surrounding the mechanistic contributions of deafferentation to ensuing neuropathic pain syndromes. Deafferentation pain has also been described for loss of other body parts (e.g., eyes and breasts) and may contribute to between 10% and upwards of 30% of neuropathic symptoms in peripheral neuropathies. There is no pathognomonic test or sign to identify deafferentation pain, and part of the controversy surrounding it stems from the prodigious challenges in differentiating cause and effect. For example, it is unknown whether cortical reorganization causes pain or is a byproduct of pathoanatomical changes accompanying injury, including pain. Similarly, ascertaining whether deafferentation contributes to neuropathic pain, or whether concomitant injury to nerve fibers transmitting pain and touch sensation leads to a deafferentation-like phenotype can be clinically difficult, although a detailed neurologic examination, functional imaging, and psychophysical tests may provide clues. Due in part to the concurrent morbidities, the physical, psychologic, and by extension socioeconomic costs of disorders associated with deafferentation are higher than for other chronic pain conditions. Treatment is symptom-based, with evidence supporting first-line antineuropathic medications such as gabapentinoids and antidepressants. Studies examining noninvasive neuromodulation and virtual reality have yielded mixed results.
The Relationship Between Intra-articular Fracture Energy and a Patient's Inflammatory Response
Authors: Haller Justin M. , Fink Diane , Smith Hannah , Olsen Zachary , Jacobs Cale , Anderson Donald
Published: March 2024

OBJECTIVES:

Prior studies have demonstrated elevated inflammatory cytokine concentrations in the synovial fluid of articular fracture patients postinjury. Similarly, CT-based fracture energy measurements have been correlated with posttraumatic osteoarthritis risk after pilon fracture. The purpose of this study was to determine the associations between synovial fluid cytokine levels, fracture energy, and overall trauma to the body in articular fracture patients.

METHODS:

Acute tibial plateau, tibial plafond, and rotational ankle fracture patients were prospectively enrolled from December 2011 through January 1, 2019. Synovial fluid concentrations of interleukin-1 beta, interleukin-1 receptor antagonist, IL-6, IL-8, IL-10, matrix metallopeptidase-1, MMP-3, and MMP-13 were quantified. Patient CT scans were used to calculate fracture energy. The Injury Severity Score (ISS) was used to relate cytokine levels to whole-body injury severity. Spearman rho correlation coefficients were calculated to assess the relationship between injury severity metrics and synovial fluid cytokine, chemokine, and matrix metallopeptidase concentrations.

RESULTS:

Eighty-seven patients were enrolled with 42 had a tibial plateau fractures (OTA/AO 41B1-2, 41B2-14, 41B3-3, 41C1-3, 41C2-4, 41C3-16), 24 patients had a tibial plafond fracture (OTA/AO 43B1-2, 43B2-4, 43B3-5, 43C1-2, 43C2-3, 43C3-8), and 21 had a rotational ankle fracture (OTA/AO 44B1-3, 44B2-3, 44B3-6, 44C1-4, 44C2-5). Fracture energy significantly differed between fracture patterns, with ankle fractures involving substantially less fracture energy (median = 2.92 J) than plafond (10.85 J, P < 0.001) and plateau fractures (13.05 J, P < 0.001). After adjustment for multiple comparisons, MMP-3 was significantly correlated with transformed fracture energy (r = 0.41, 95% confidence interval [CI], 0.22–0.58, P < 0.001), while IL-1β was significantly correlated with the Injury Severity Score (Spearman ρ = 0.31, 95% CI, 0.08–0.49, P = 0.004).

CONCLUSIONS:

Synovial fluid MMP-3 concentration was significantly correlated with CT-quantified fracture energy in intra-articular fracture patients. Given that in clinical practice fracture energy tends to correlate with posttraumatic osteoarthritis risk, MMP-3 may warrant further investigation for its role in posttraumatic osteoarthritis development after articular fracture.

LEVEL OF EVIDENCE:

Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Psychometric properties of the Turkish version of Central Sensitization Inventory-9 in patients with chronic musculoskeletal pain
Authors: Bazancir-Apaydin Zilan , Sari Fulden
Published: March 2024

The aim of the study was to assess the psychometric properties of the Turkish version of Central Sensitization Inventory-9 (CSI-9) in patients with chronic musculoskeletal pain. The methodological study included 92 patients with chronic musculoskeletal pain. The original version of the CSI-9 was translated and culturally adapted into Turkish. The internal consistency and test-retest reliability were evaluated with Cronbach’s α and the intraclass correlation coefficient (ICC), respectively. The assessment of reproducibility was conducted with the standard error of measurement (SEM) and minimal detectable difference (MDD) values. Convergent validity was explored by correlation analysis between the CSI-9 and Central Sensitization Inventory (CSI-25), Brief Pain Inventory (BPI), and European Quality of Life Survey-5 Dimensions (EQ-5D). The structural validity was assessed with factor analysis. Floor and ceiling effects were also analyzed. We found a very good internal consistency (Cronbach’s α of 0.83) and excellent test-retest reliability (ICC of 0.96) of the Turkish CSI-9. The SEM demonstrated a range between 0.19 and 1.12, and the MDD was observed to vary from 1.17 to 1.35. The CSI-9 correlated significantly with the CSI-25 (r = 0.77, P < 0.001), the pain severity subscale of the BPI (r = 0.41 to 0.53, P < 0.001), the pain interference subscale of the BPI (r = 0.21 to 0.58, P = 0.02 to P < 0.001), the EQ-5D (r = 0.24 to 0.48, P < 0.05), and the EQ-5D visual analog scale (r = −0.41, P < 0.001). One factor was identified within the CSI-9. Our data suggest that the Turkish CSI-9 is reliable and valid outcome measure for assessing CS in patients with chronic musculoskeletal pain.
Reframing the Morbidity and Mortality Conference: The Impact of a Just Culture
Authors: Brook Karolina , Agarwala Aalok V. , Tewfik George L.
Published: March 2024

Morbidity and mortality (M&M) conferences are prevalent in all fields of medicine. Historically, they arose out a desire to improve medical care. Nevertheless, the goals of M&M conferences are often poorly defined, at odds with one another, and do not support a just culture. We differentiate among the various possible goals of an M&M and review the literature for strategies that have been shown to achieve these goals. Based on the literature, we outline an ideal M&M structure within the context of just culture: The process starts with robust adverse event and near miss reporting, followed by careful case selection, excluding cases solely attributable to individual error. Prior to the M&M, the case should be openly discussed with involved members and should be reviewed using a selected framework. The goal of the M&M should be selected and clearly defined, and the presentation format and rules of conduct should all conform to the selected presentation goal. The audience should ideally be multidisciplinary and multispecialty. The M&M should conclude with concrete tasks and assigned follow-up. The entire process should be conducted in a peer review protected format within an environment promoting psychological safety. We conclude with future directions for M&Ms.
Science in Schools: combining language and microbiology engagement during a pandemic
Authors: Pascoe Michael John , Brown Helen Louise
Published: March 2024

This paper presents an public engagement pedagogy designed to engage Key Stage-one and -two students. The activities were developed for a British Council Science-in-Schools visit, allowing UK-based researchers to visit French territory schools, delivering activities in English. Focusing on infection transmission, our event aimed to enhance understanding of infection transmission concepts (coughing, sneezing, handwashing and surface contamination). Additionally, we hosted a "masterclass" session for teachers, demonstrating the activities and discussing their integration into classroom settings.
Here we present lesson plans for both student- and teacher-focused sessions and detailed protocol and demonstration video for each activity. We also include vocabulary lists and flashcards which were used within the sessions to aid student comprehension of the activities and support further discussion around key concepts and findings. Finally, we present a brief reflective evaluation of the visit and offer considerations for others wishing to use the materials as part of their pedagogy practice.
There was a positive reception to the activities among both students and teachers. Here the activities were used with French-speaking students developing English language skills, but we believe that these activities could be used with a wide range of ages, scientific literacy and event types.
In conclusion, this paper underscores the significance of public engagement pedagogy in fostering health literacy and empowering young learners to make informed decisions regarding personal and community well-being. By combining interactive methodologies with targeted public health interventions, we aim to inspire a generation of proactive global citizens equipped to address contemporary health challenges.
Characteristics of soil origin Pseudomonas batumici Koz11 isolated from a remote island in Japan
Authors: Zuo Hui , Morimoto Yuh , Baba Tadashi
Published: March 2024

Soil samples from a remote Japanese island (Kozushima) were processed and investigated for organisms exhibiting antimicrobial activity against pathogenic strains. A Pseudomonas strain demonstrating antimicrobial activity against Staphylococcus aureus (S. aureus) was observed, leading to further investigation. Whole-genome sequencing was used to identify species and phylogenetic analysis, followed by in silico molecular analysis. Chemotaxonomic and biochemical analyses were conducted to characterize the strain further. Genomic analysis identified a strain of interest, Pseudomonas batumici (P. batumici), a strain initially isolated from soil of the Black Sea coast of the Caucasus in 1980. P. batumici Koz11 is the second P. batumici strain isolated and identified outside the area where it was first found. Similar to the type strain, P. batumici Koz11 showed antimicrobial activity against various S. aureus strains, including vancomycin-resistant S. aureus. However, the previously reported gene cluster known as the "batumin gene cluster," which synthesizes antimicrobial compounds, was absent from P. batumici Koz11. This study provides insights on P. batumici that were not previously known. Since the type of strain of P. batumici is exclusively deposited in the Ukrainian Collection of Microorganisms, the Koz11 strain may be a surrogate to facilitate continued study of P. batumici.
Maternal Alcohol Drinking Patterns Predict Offspring Neurobehavioral Outcomes
Authors: Myrick Abbey , Jimenez Diane , Jacquez Belkis , Sun Melody S. , Noor Shahani , Milligan Erin D. , Valenzuela C. Fernando , Linsenbardt David N.
Published: March 2024

SIGNIFICANCE

The timing, rate, and quantity of gestational alcohol consumption, collectively referred to here as Maternal Drinking Patterns (MDPs), are of known importance to fetal developmental outcomes. Though studies in rodents exist that have investigated the impact of gestational alcohol drinking characteristics, few have sought to determine the impact of MDPs on offspring behavioral outcomes.

METHODS

We first used specialized equipment to record the precise amount and timing of binge alcohol consumption in pregnant mouse dams, and then characterized MDPs using Principle Component Analysis (PCA). We focused these analyses on the first fifteen minutes of every gestational drinking session when dams consumed the majority of each session’s alcohol (a phenomenon known as front-loading), as well as the entire 2 hour session across all days of gestation. We next tested offspring in open field and rotarod assays and evaluated these behavioral results in the context of MDPs.

RESULTS

Male alcohol exposed mice exhibited longer latencies to fall on the rotarod compared to their controls, which we attribute to a delayed decrease in body weight-gain not observed in females. This effect was found to be associated with MDPs within the first fifteen minutes of drinking, but not other MDPs. Female alcohol exposed mice had significantly reduced total locomotor activity in the open field compared to controls, and this effect was also associated with MDPs but only of the entire drinking session. Surprisingly, total gestational alcohol consumption alone was not associated with any particular behavioral outcome. Furthermore, we replicated robust behavioral data demonstrating development of allodynia in alcohol exposed mice where it did not develop in controls.

CONCLUSIONS

To our knowledge, this report represents the highest resolution assessment of alcohol drinking throughout gestation, and one of few to have identified relationships between specific alcohol MDPs and neurobehavioral outcomes in offspring. Specifically, based on characteristics of the PCA groups, we found evidence that the rate of alcohol front-loading leads to developmental delays in males, whereas an interaction of front-loading rate and duration, overall persistence, and total amount consumed lead to a female-only decrease in locomotor activity. Beyond these results, we provide a method for precise and accessible tracking of such data.
Motor Hotspot Localization Based on Electroencephalography Using Convolutional Neural Network in Patients with Stroke
Authors: Choi Ga-Young , Seo Jeong-Kweon , Kim Kyoung Tae , Chang Won Kee , Paik Nam-Jong , Kim Won-Seok , Hwang Han-Jeong
Published: March 2024

Background

Although transcranial magnetic stimulation (TMS) is the optimal tool for identifying individual motor hotspots for transcranial electrical stimulation (tES), it requires a cumbersome procedure in which patients must visit the hospital each time and rely on expert judgment to determine the motor hotspot. Therefore, in previous study, we proposed electroencephalography (EEG)-based machine learning approach to automatically identify individual motor hotspots. In this study, we proposed an advanced EEG-based motor hotspot identification algorithm using a deep learning model and assessed its clinical feasibility and benefits by applying it to stroke patient EEGs.

Methods

EEG data were measured from thirty subjects as they performed a simple hand movement task. We utilized the five types of input data depending on the processing levels to assess the signal processing capability of our proposed deep learning model. The motor hotspot locations were estimated using a two-dimensional convolutional neural network (CNN) model. The error distance between the 3D coordinate information of the individual motor hotspots identified by the TMS (ground truth) and EEGs was calculated using the Euclidean distance. Additionally, we confirmed the clinical benefits of our proposed deep-learning algorithm by applying the EEG of stroke patients.

Results

A mean error distance between the motor hotspot locations identified by TMS and our approach was 2.34 ± 0.19 mm when using raw data from only 9 channels around the motor area. When it was tested on stroke patients, the mean error distance was 1.77 ± 0.15 mm using only 5 channels around the motor area.

Conclusion

We have demonstrated that an EEG-based deep learning approach can effectively identify the individual motor hotspots. Moreover, we validated the clinical benefits of our algorithm by successfully implementing it in stroke patients. Our algorithm can be used as an alternative to TMS for identifying motor hotspots and maximizing rehabilitation effectiveness.
NeuralPlayground: A Standardised Environment for Evaluating Models of Hippocampus and Entorhinal Cortex
Authors: Dominé Clémentine C. J. , Carrasco-Davis Rodrigo , Hollingsworth Luke , Sirmpilatze Nikoloz , Tyson Adam L. , Jarvis Devon , Barry Caswell , Saxe Andrew M.
Published: March 2024

Neural processes in the hippocampus and entorhinal cortex are thought to be crucial for spatial cognition. A growing variety of theoretical models have been proposed to capture the rich neural and behavioral phenomena associated with these circuits. However, systematic comparison of these theories, both against each other and against empirical data, remains challenging. To address this gap, we present NeuralPlayground, an open-source standardised software framework for comparisons between theory and experiment in the domain of spatial cognition. This Python software package offers a reproducible way to compare models against a centralised library of published experimental results, including neural recordings and animal behavior. The framework implements threeAgentsembodying different computational models; threeExperimentscomprising publicly available neural and behavioral datasets; a customisable 2-dimensionalArena(continuous and discrete) able to generate common and novel spatial layouts; and aComparisontool that facilitates systematic comparisons between models and data. Each module can also be used separately, allowing standardised and flexible access to influential models and data sets. We hope NeuralPlayground, available on GitHub3, provides a starting point for a shared, standardized, open, and reproducible computational understanding of the role of the hippocampus and entorhinal cortex in spatial cognition.
HSV-1 infection induces a downstream shift of the +1 nucleosome
Authors: Weiß Elena , Whisnant Adam W. , Hennig Thomas , Djakovic Lara , Dölken Lars , Friedel Caroline C.
Published: March 2024

Herpes simplex virus 1 (HSV-1) infection induces a loss of host transcriptional activity and widespread disruption of host transcription termination, which leads to an induction of open chromatin downstream of genes. In this study, we show that lytic HSV-1 infection also leads to an extension of chromatin accessibility at promoters into downstream regions. This is most prominent for highly expressed genes and independent of the immediate-early proteins ICP0, ICP22, and ICP27 and the virion host shutoff proteinvhs.ChIPmentation of the noncanonical histone variant H2A.Z, which is strongly enriched at +1 and −1 nucleosomes, indicated that these chromatin accessibility changes are linked to a downstream shift of +1 nucleosomes. In yeast, downstream shifts of +1 nucleosomes are induced by RNA Polymerase II (Pol II) degradation. Accordingly, irreversible depletion of Pol II from genes in human cells using α-amanitin altered +1 nucleosome positioning similar to lytic HSV-1 infection. Consequently, treatment with phosphonoacetic acid (PAA) and knockout of ICP4, which both prevent viral DNA replication and alleviate the loss of Pol II from host genes, largely abolished the downstream extension of accessible chromatin in HSV-1 infection. In the absence of viral DNA replication, doxycycline-induced expression of ICP27, which redirects Pol II from gene bodies into intergenic regions by disrupting transcription termination, induced an attenuated effect that was further enhanced by co-expression of ICP22. In summary, our study provides strong evidence that HSV-1-induced depletion of Pol II from the host genome leads to a downstream shift of +1 nucleosomes at host promoters.

Importance

Lytic herpes simplex virus 1 (HSV-1) infection leads to a profound host transcription shutoff. Loss of RNA Polymerase II (Pol II) in yeast has previously been shown to relax +1 nucleosome positioning to more thermodynamically favorable sites downstream of transcription start sites. Here, we show that a similar phenomenon is likely at play in lytic HSV-1 infection. Sequencing of accessible chromatin revealed a widening of nucleosome-free regions at host promoters into downstream regions. By mapping genome-wide positions of the noncanonical histone variant H2A.Z enriched at +1 and −1 nucleosomes, we demonstrate a downstream shift of +1 nucleosomes for most cellular genes in lytic HSV-1 infection. As chemical depletion of Pol II from genes also leads to a downstream shift of +1 nucleosomes in human cells, changes in chromatin architecture at promoters in HSV-1 infection are likely a consequence of HSV-1-induced loss of Pol II activity from the host genome.
The protective roles of Eugenol on type 1 diabetes mellitus through NRF2 mediated oxidative stress pathway
Authors: Jiang Yalan , He Pingping , Sheng Ke , Peng Yongmiao , Wu Huilan , Qian Songwei , Ji Weiping , Guo Xiaoling , Shan Xiaoou
Published: March 2024

Type 1 diabetes mellitus (T1DM), known as insulin-dependent diabetes mellitus, is characterized by persistent hyperglycemia resulting from damage to the pancreatic β cells and an absolute deficiency of insulin, leading to multi-organ involvement and a poor prognosis. The progression of T1DM is significantly influenced by oxidative stress and apoptosis. The natural compound eugenol (EUG) possesses anti-inflammatory, anti-oxidant, and anti-apoptotic properties. However, the potential effects of EUG on T1DM had not been investigated. In this study, we established the streptozotocin (STZ)-induced T1DM mouse modelin vivoand STZ-induced pancreatic β cell MIN6 cell modelin vitroto investigate the protective effects of EUG on T1DM, and tried to elucidate its potential mechanism. Our findings demonstrated that the intervention of EUG could effectively induce the activation of nuclear factor E2-related factor 2 (NRF2), leading to an up-regulation in the expressions of downstream proteins NQO-1 and HO-1, which are regulated by NRF2. Moreover, this intervention exhibited a significant amelioration in pancreatic β cell damage associated with T1DM, accompanied by an elevation in insulin secretion and a reduction in the expression levels of apoptosis and oxidative stress related markers. Furthermore, ML385, an NRF2 inhibitor, reversed these effects of EUG. The present study suggested that EUG exerted protective effects on pancreatic β cells in T1DM by attenuating apoptosis and oxidative stress through the activation of the NRF2 signaling pathway. Consequently, EUG holds great promise as a potential therapeutic candidate for T1DM.
Microbial Response to Natural Disturbances: Rare Biosphere often plays a role
Authors: Zhao Jianshu , Brandt Genevieve , Wang Zhao , Hunt Dana E. , Rodriguez-R Luis M. , Hatt Janet K. , Konstantinidis Konstantinos T.
Published: March 2024

Understanding how microbial populations respond to disturbances represents a major goal for microbial ecology. While several theories have been advanced to explain microbial community compositional changes in response to disturbances, appropriate data to test these theories is scarce, especially when considering the challenges to define rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to define rare populations, and by borrowing concepts from macroecology, the proportional similarity index (PS index), to define generalists. Using these concepts, we found that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm weather events snaps-in part-due to the response of rare populations, providing support for the insurance hypothesis (i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbances). Generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis, i.e., disturbance favors generalists. Taken together, our results advance understanding of the mechanisms governing microbial populations dynamics under changing environmental conditions and have potential applications for ecosystem management.
Studying relative RNA localization From nucleus to the cytosol
Authors: Ntasis Vasilis F. , Guigó Roderic
Published: March 2024

The precise coordination of important biological processes, such as differentiation and development, is highly dependent on the regulation of expression of the genetic information. The flow of the genetic information is tightly regulated on multiple levels. Among them, RNA export to cytosol is an essential step for the production of proteins in eukaryotic cells. Hence, estimating the relative concentration of RNA molecules of a given transcript species in the nucleus and in the cytosol is of major significance as it contributes to the understanding of the dynamics of RNA trafficking between the nucleus and the cytosol. The most efficient way to estimate the levels of RNA species genome-wide is through RNA sequencing (RNAseq). While RNAseq can be performed separately in the nucleus and in the cytosol, because measured transcript levels are relative to the total volume of RNA in these compartments, and because this volume is usually unknown, the transcript levels in the nucleus and in the cytosol cannot be directly compared. Here we show theoretically that if, in addition to nuclear and cytosolic RNA-seq, whole cell RNA-seq is also performed, then accurate estimations of the localization of transcripts can be obtained. Based on this, we designed a method that estimates, first the fraction of the total RNA volume in the cytosol (nucleus), and then, this fraction for every transcript. We evaluate our methodology on simulated data and nuclear and cytosolic single cell data available. Finally, we use our method to investigate the cellular localization of transcripts using bulk RNAseq data from the ENCODE project.
TRPC6 is a mechanosensitive channel essential for ultrasound neuromodulation in mammalian brain
Authors: Matsushita Yumi , Yoshida Kaede , Yoshiya Miyuki , Shimizu Takahiro , Tsukamoto Satoshi , Takeuchi Yuichi , Higuchi Makoto , Shimojo Masafumi
Published: March 2024

Ultrasound neuromodulation has become an innovative technology that enables non-invasive intervention in mammalian brain circuits with high spatiotemporal precision. Despite the expanding utility of ultrasound neuromodulation in the neuroscience research field and clinical applications, the molecular and cellular mechanisms by which ultrasound impacts neural activity in the brain are still largely unknown. Here, we report that transient receptor potential canonical 6 (TRPC6), a mechanosensitive non-selective cation channel, is essential for ultrasound neuromodulation of mammalian neuronsin vitroandin vivo. We first demonstrated that ultrasound irradiation elicited rapid and robust Ca2+transients mediated via extracellular Ca2+influx in cultured mouse cortical and hippocampal neurons. Ultrasound-induced neuronal responses were massively diminished by blocking either the generation of action potential or synaptic transmission. Importantly, both pharmacological inhibition and genetic deficiency of TRPC6 almost completely abolished neuronal responses to ultrasound. Furthermore, we found that intracerebroventricular administration of a TRPC6 blocker significantly attenuated the population of neuronal firings in the cerebral cortex evoked by transcranial ultrasound irradiation in mice. Our findings indicate that TRPC6 is an indispensable molecule of ultrasound neuromodulation in the intact mammalian brains, providing fundamental understanding of biophysical molecular mechanisms of ultrasound neuromodulation as well as insight into its future feasibility in neuroscience and translational researches in humans.
Application of mechanistic multiparameter optimization and large scale in vitro toin vivopharmacokinetics correlations to small molecule therapeutic projects
Authors: Broccatelli Fabio , Veeravalli Vijayabhaskar , Cashion Daniel , Baylon Javier L. , Lombardo Franco , Jia Lei
Published: March 2024

Computational chemistry and machine learning are used in drug discovery to predict target-specific and pharmacokinetic properties of molecules. Multiparameter optimization (MPO) functions are used to summarize multiple properties into a single score, aiding compound prioritization. However, over-reliance on subjective MPO functions risks reinforcing human bias. Mechanistic modeling approaches based on physiological relevance can be adapted to meet different potential key objectives of the project (e.g. minimizing dose, maximizing safety margins and/or minimized drug-drug interaction risk) while retaining the same underlying model structure. The current work incorporates recent approaches to predictin vivoPK properties and validatesin vitrotoin vivocorrelation analysis to support mechanistic PK MPO. Examples of use and impact in small molecule drug discovery projects are provided. Overall, the mechanistic MPO identifies 83% of the compounds considered as short-listed for clinical experiments in the top 2ndpercentile, and 100% in the top 10thpercentile, resulting in an area under the receiver operating characteristic curve (AUCROC) > 0.95. In addition, the MPO score successfully recapitulates the chronological progression of the optimization process across different scaffolds. Finally, the MPO scores for compounds characterized in pharmacokinetics experiments are markedly higher compared to the rest of the compounds synthesized, highlighting the potential of this tool to reduce the reliance onin vivotesting for compound screening.
Spatial targeting of the prostaglandin receptor EP2 to very early endosomes co-ordinates PGE2-mediated cAMP signaling in decidualizing human endometrium
Authors: Brighton Paul J. , Walker Abigail R. , Mann Oliver , Kong Chow-Seng , Lucas Emma S. , Vrljicak Pavle , Brosens Jan J. , Hanyaloglu Aylin C.
Published: March 2024

Decidualization denotes the differentiation of endometrial stromal cells into specialized decidual cells, essential for embryo implantation and pregnancy. The process requires coordinated activation of both progesterone and cAMP signaling pathways, which converge on downstream transcription factors. PGE2 and relaxin, acting respectively through their Gαs-coupled GPCRs EP2 and RXFP1, are putative candidates responsible for generating cAMP in differentiating stromal cells. Here, we show that PGE2 is less efficacious than relaxin in elevating intracellular cAMP levels in primary stromal cells but more effective at driving the expression of canonical decidual genes. Both PGE2- and relaxin-induced cAMP generation involves receptor internalization, but EP2 is endocytosed into very early endosomes (VEEs). Perturbation of the VEE machinery dysregulates PGE2-dependent cAMP profiles and disrupts key decidual signaling pathways, resulting in a disordered differentiation response. We demonstrate that the spatial location of EP2 is essential for coordinated activation of the downstream signaling cascades that govern decidualization.
Cortical lipids containing choline mediate cannabinoid-induced cognitive improvement
Authors: Moreno-Rodríguez Marta , Martínez-Gardeazabal Jonatan , de Tena Iker Bengoetxea , Llorente-Ovejero Alberto , Lombardero Laura , de San Román Estibaliz González , Giménez-Llort Lydia , Manuel Iván , Rodríguez-Puertas Rafael
Published: March 2024

Recent research connecting choline-containing lipids to basal forebrain cholinergic neurons (BFCN) degeneration in neuropathological states highlights a challenge for balancing lipid integrity with optimal acetylcholine (ACh) levels. Warranting an adequate choline source to maintain ACh levels in this pathway is crucial for preserving memory. The endocannabinoid (eCB) system plays a role in modulating learning and memory processes controlled by cholinergic neurotransmission. Consequently, we propose that activation of this system is neuroprotective against cholinergic degeneration. In the present study, we investigated the neuroprotective effect of a subchronic treatment with the CB1cannabinoid agonist, WIN55,212-2, using bothex vivoandin vivo192IgG-Saporin models of specific cholinergic damage. Degeneration of baso-cortical cholinergic pathways induced memory deficits and a downregulation of saturated and mono-unsaturated lysophosphatidylcholines (LPC) cortical levels. WIN55,212-2 not only restored memory deficits but also increased cortical ACh levels and modified cortical choline-containing lipids such as sphingomyelins (SM) and LPCs, which are essential for correct memory functioning, in lesioned animals. Given these results, we propose that WIN55,212-2 generates an alternative choline source through the breakdown of SMs, which is enough to increase cortical ACh levels and LPCs. These findings suggest that modification of choline-containing lipids by the activation of CB1receptors is a promising therapy for dementia associated with cholinergic dysfunction, such as in Alzheimer’s disease (AD).
Comparative transcriptomic and lipidomic analysis of fatty acid accumulation in threeCamellia oleiferavarieties during maturation
Authors: Yang Dayu , Wang Rui , Lai Hanggui , Chen Yongzhong , He Yimin , Xun Chengfeng , Zhang Ying , He Zhilong
Published: March 2024

Camellia oleiferastands out as one of China’s leading woody oil crops, famed for its tea oil, which boasts a high content of unsaturated fatty acids. Often referred to as "liquid gold" or "Oriental olive oil," this oil is prized for its nutritional benefits and culinary versatility, marking Camellia oleifera as a valuable agricultural and economic resource. This study provides an integrated investigation of the transcriptome and lipidome within seeds at the maturation stage across threeC. oleiferavarieties, revealing a significant relationship between fatty acid production and genes involved in lipid synthesis. Through transcriptomic analysis, 26,344 genes with varied expression were found. Functional enrichment analysis highlighted that pathways related to starch and sucrose metabolism, plant hormone signal transduction, and lipid accumulation were highly enriched among the differentially expressed genes. Additionally, expression variations ofSADandFADsamong different varieties were explored. The analysis suggests that increased expression of genes such asFAD3,FAD7, andFAD8during the maturation stage may enhance the proportion of linolenic acid while reducing oleic acid content. This alteration could potentially stimulate fatty acid synthesis through a feedback regulation mechanism, thereby enhancing seed oil content. These findings provide a novel perspective on the feedback regulation mechanisms underlying lipid biosynthesis inC. oleiferaseeds, offering significant insights to boost oil yield and improve tea oil quality.
Estimating evolutionary and demographic parameters via ARG-derived IBD
Authors: Huang Zhendong , Kelleher Jerome , Chan Yao-ban , Balding David J.
Published: March 2024

Inference of demographic and evolutionary parameters from a sample of genome sequences often proceeds by first inferring identical-by-descent (IBD) genome segments. By exploiting efficient data encoding based on the ancestral recombination graph (ARG), we obtain three major advantages over current approaches: (i) no need to impose a length threshold on IBD segments, (ii) IBD can be defined without the hard-to-verify requirement of no recombination, and (iii) computation time can be reduced with little loss of statistical efficiency using only the IBD segments from a set of sequence pairs that scales linearly with sample size. We first demonstrate powerful inferences when true IBD information is available from simulated data. For IBD inferred from real data, we propose an approximate Bayesian computation inference algorithm and use it to show that poorly-inferred short IBD segments can improve estimation precision. We show estimation precision similar to a previously-published estimator despite a 4 000-fold reduction in data used for inference. Computational cost limits model complexity in our approach, but we are able to incorporate unknown nuisance parameters and model misspecification, still finding improved parameter inference.

Author summary

Samples of genome sequences can be informative about the history of the population from which they were drawn, and about mutation and other processes that led to the observed sequences. However, obtaining reliable inferences is challenging, because of the complexity of the underlying processes and the large amounts of sequence data that are often now available. A common approach to simplifying the data is to use only genome segments that are very similar between two sequences, called identical-by-descent (IBD). The longer the IBD segment the more informative about recent shared ancestry, and current approaches restrict attention to IBD segments above a length threshold. We instead are able to use IBD segments of any length, allowing us to extract much more information from the sequence data. To reduce the computation burden we identify subsets of the available sequence pairs that lead to little information loss. Our approach exploits recent advances in inferring aspects of the ancestral recombination graph (ARG) underlying the sample of sequences. Computational cost still limits the size and complexity of problems our method can handle, but where feasible we obtain dramatic improvements in the power of inferences.
SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects
Authors: Ruiz Baptiste , Belcour Arnaud , Blanquart Samuel , Buffet-Bataillon Sylvie , Hüerou-Luron Isabelle Le , Siegel Anne , Cunff Yann Le
Published: March 2024

The composition of the gut microbiota is a known factor in various diseases, and has proven to be a strong basis for automatic classification of disease state. A need for a better understanding of this community on the functional scale has since been voiced, as it would enhance these approaches’ biological interpretability. In this paper, we have developed a computational pipeline for integrating the functional annotation of the gut microbiota to an automatic classification process, and facilitating downstream interpretation of its results. The process takes as input taxonomic composition data (such as tables of Operational Taxonomic Unit (OTU) or Amplicon Sequence Variant (ASV) abundances), and links each component to its functional annotations through interrogation of the UniProt database. A functional profile of the gut microbiota is built from this basis. Both profiles, microbial and functional, are used to train Random Forest classifiers to discern unhealthy from control samples. An automatic variable selection is then performed on the basis of variable importance, and the method can be iterated until classification performances diminish. This process shows that the translation of the microbiota into functional profiles gives comparable, albeit slightly inferior performances when compared to microbial profiles. Through repetition, it also outputs a robust subset of discriminant variables. These selections were shown to be more reliable than those obtained by a state of the art method, and its contents were validated through a manual bibliographic research. The interconnections between selected OTUs and functional annotations were also analyzed, and revealed that important annotations emerge from the cumulated influence of non-selected OTUs.
Prioritizing the Valorization Strategies of an Invasive Fern (Azolla) in a Wetland
Authors: Nikkhah Farima , Ramezanian Mohammad Rahim , Rosentrater Kurt A.
Published: March 2024

Wetlands play a vital role as one of the most important natural habitats on our planet. However, the survival of these natural wetlands is threatened by various factors. The arrival of invasive and non-native aquatic ferns is one of these challenges. In this regard, Azolla filiculoides has become a severe problem for the Anzali wetland. Azolla, as an aquatic fern, has created numerous issues in aquatic habitats and paddy fields in recent decades. However, the valorization of Azolla can contribute to the establishment of a collection system for this invasive fern, which can consequently reduce the negative impact of this fern on the wetland, and it can serve as a free and available source of biomass. In this respect, a fuzzy multi-criteria decision-making approach was used to rank the valorization strategies of this invasive fern. Initially, through an in-depth literature review and expert opinions, four criteria were designated as indicators for research evaluation: 1) technical, 2) economic, 3) social, and 4) environmental. Six management options for Azolla were considered: 1) no collection, 2) collection and landfilling, 3) direct use as livestock and poultry feed, 4) composting, 5) biogas generation, and 6) biodiesel generation. The results revealed that “biodiesel generation,” “biogas generation,” and “composting” were ranked as the most effective management strategies for Azolla in the investigated wetland. This study suggests that bioenergy generation and compost production from Azolla are promising strategies towards mitigating the negative impact of this fern on the Anzali wetland.
Enhancing viscosity control in antibody formulations: A framework for the biophysical screening of mutations targeting solvent-accessible hydrophobic and electrostatic patches
Authors: Armstrong Georgina B , Shah Vidhi , Sanches Paula , Patel Mitul , Casey Ricky , Jamieson Craig J , Burley Glenn A , Lewis William J , Rattray Zahra
Published: March 2024

The formulation of high-concentration monoclonal antibody (mAb) solutions in low dose volumes for autoinjector devices poses challenges in manufacturability and patient administration due to elevated solution viscosity. In the current study, we present a systematic experimental framework for the computational screening of molecular descriptors to guide the design of mutants with modified viscosity profiles accompanied by experimental evaluation. Our observations using a model anti-IL8 antibody reveal that the reduction in viscosity is influenced by the location of hydrophobic interactions, while targeting positively charged patches in mAb1 leads to the most significant viscosity increase compared to the wild-type mAb. We conclude that existingin silicopredictions of physicochemical properties exhibit poor correlation with experimental parameters for antibodies with suboptimal developability characteristics, emphasizing the necessity for comprehensive case-by-case evaluations of mAbs. This approach aids in the rational design of mAbs with tailored solution viscosities, ensuring improved manufacturability and patient convenience in self-administration scenarios.
Sustained neurotrophic factor cotreatment enhances donor and host retinal ganglion cell survival in mice
Authors: Soucy Jonathan R. , Kriukov Emil , Oswald Julia , Phay Monichan , Masland John , Pernstich Christian , Baranov Petr
Published: March 2024

Retinal ganglion cells (RGCs) lack regenerative capacity in mammals, and their degeneration in glaucoma leads to irreversible blindness. The transplantation of stem cell-derived RGCs lacks clinically relevant effect due to insufficient survival and integration of donor cells. We hypothesize that the retinal microenvironment plays a critical role in this process, and we can engineer a more acceptable setting for transplantation. Since the adult mammalian retina does not have regenerative capacity, we turned to the developing human retina to reconstruct cell-cell interactions at a single-cell level. We established a human fetal retina atlas by integrating currently available single-cell RNA sequencing datasets of human fetal retinas into a unified resource. We align RGC transcriptomes in pseudotime to map RGC developmental fate trajectories against the broader timeline of retinal development. Through this analysis, we identified brain-derived neurotrophic factor (BDNF) and glial-derived neurotrophic factor (GDNF) as key factors in RGC survival, highly expressed during fetal development but significantly reduced in adulthood despite the persistence of their receptors. To demonstrate the practical application of these findings, we show that using a slow-release formulation of BDNF and GDNF enhances RGC differentiation, survival, and function in vitro and improves RGC transplantation outcomes in a mouse model. BNDF/GDNF co-treatment not only increased survival and coverage of donor RGCs within the retina but also showed neuroprotective effects on host RGCs, preserving retinal function in a model of optic neuropathy. Altogether, our findings suggest that manipulating the retinal microenvironment with slow-release neurotrophic factors holds promise in regenerative medicine for treating glaucoma and other optic neuropathies. This approach not only improves donor cell survival and integration but also provides a neuroprotective benefit to host cells, indicating a significant advancement for glaucoma therapies.