bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explainable machine learning for the identification of proteome states via the data processing kitchen sink
Authors: Scott Aaron M. , Hartman Erik , Malmström Johan , Malmström Lars 
Published: September 2023

AbstractThe application of machine learning algorithms to facilitate the understanding of changes in proteome states has emerged as a promising methodology in proteomics research. Unfortunately, these methods can prove difficult to interpret, as it may not be immediately obvious how models reach their predictions. We present the data processing kitchen sink (DPKS) which provides reproducible access to classic statistical methods and advanced explainable machine learning algorithms to build highly accurate and fully interpretable predictive models. In DPKS, explainable machine learning methods are used to calculate the importance of each protein towards the prediction of a model for a particular proteome state. The calculated importance of each protein can enable the identification of proteins that drive phenotypic change in a data-driven manner while classic techniques rely on arbitrary cutoffs that may exclude important features from consideration. DPKS is a free and open source Python package available athttps://github.com/InfectionMedicineProteomics/DPKS.
Rapid translocation of NGR proteins drives polarization of PIN-activating D6 protein kinase during root gravitropism
Authors: Kulich Ivan , Schmid Julia , Teplova Anastasia , Qi Linlin , Friml Jiří 
Published: September 2023

AbstractRoot gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.
Development and validation of a respiratory syncytial virus multiplex immunoassay
Authors: Marsall Patrick , Fandrich Madeleine , Griesbaum Johanna , Harries Manuela , Lange Berit ,   RESPINOW study consortium, Ascough Stephanie , Dayananda Pete , Chiu Christopher , Remppis Jonathan , Ganzenmueller Tina , Renk Hanna , Strengert Monika , Schneiderhan-Marra Nicole , Dulovic Alex 
Published: September 2023

AbstractRespiratory syncytial virus (RSV) is one of the leading causes of severe respiratory disease in infants and adults. RSV exists as two subtypes A and B, which co-circulate throughout the season, although one will usually become dominant. While vaccines and monoclonal therapeutic antibodies either are or will shortly become available, correlates of protection remain unclear. For this purpose, we developed an RSV multiplex immunoassay that analyses antibody titers towards the post-F, Nucleoprotein, and a diverse mix of G proteins. Technical and clinical validation showed outstanding performance, while methodological developments enabled identification of the subtype of previous infections through use of the diverse G proteins for approximately 50% of samples. As a proof of concept to show the suitability of the assay in serosurveillance studies, we then evaluated titer decay and age- dependent antibody responses within population cohorts. Overall, the developed assay shows robust performance, is scalable, provides additional information on infection subtype, and is therefore ideally suited to be used in future population cohort studies.ImportanceAlthough respiratory syncytial virus (RSV) is endemic and re-infections are common and harmless to the majority of the population, it is a leading cause of hospitalization in young children, the elderly, or immunocompromised individuals. A better characterization of RSV immunology and spreading dynamics is thus critical for preparedness, especially when interventions aiming to mitigate other diseases (e.g., COVID-19) disturb its endemic cycles. This requires high-throughput information-dense assays. We therefore developed a bead-based multiplex immunoassay that allows measurements of antibodies against multiple RSV antigens simultaneously. We identified antibodies which were strong indicators of previous infection, while others allowed identification of the subtype of the previous infection. The assay itself was shown to be robust and scalable, making it ideal for to keep track of the temporal variation RSV immunity profiles within the population.
The olfactory-based neurofeedback of the EEG alpha rhythm
Authors: Medvedeva Alexandra , Ninenko Ivan , Kleeva Daria F , Fedoseev Alexey , Bazhenov Artem , Cabrera Miguel Altamirano , Tsetserukou Dzmitry , Lebedev Mikhail A 
Published: September 2023

AbstractNeurofeedback (NFB) is a form of biofeedback that enables subjects to monitor and control their own brain activity. To communicate with the subject, modern NFB training methodologies utilize various signaling mechanisms, typically visual and/or auditory stimuli. Olfaction has not been explored yet as a way to deliver NFB. Here we developed an olfactory-based NFB system based on electroencephalographic (EEG) recordings in human participants. The system incorporates an EEG recording apparatus, a custom olfactory display for the automated delivery of Sniffin’ Sticks, and a Python application for the conversion of EEG rhythms into NFB signals and controlling behavioral tasks. We tested occipital alpha rhythm as the source of NFB. Fifteen healthy participants were randomly assigned to three groups: olfactory neurofeedback, auditory NFB, and mock-olfactory NFB. NFB training resulted in an increase of alpha power in the true NFB groups, but not in the mock NFB group where the alpha power decreased, probably because of fatigue and drowsiness. Based on these results, we conclude that olfactory NFB is feasible, and lay out a framework for its future development.
Genome-wide CRISPRi screens reveal the essentialome and determinants for susceptibility to dalbavancin inStaphylococcus aureus
Authors: Liu Xue , de Bakker Vincent , Heggenhougen Maria Victoria , Mårli Marita Torrissen , Frøynes Anette Heidal , Salehian Zhian , Porcellato Davide , Angeles Danae Morales , Veening Jan-Willem , Kjos Morten 
Published: September 2023

AbstractAntibiotic resistance and tolerance remain a major problem for treatment of staphylococcal infections. Knowing genes that influence antibiotic susceptibility could open the door to novel antimicrobial strategies, including targets for new synergistic drug combinations. Here, we developed a genome-wide CRISPR interference library forStaphylococcus aureus, demonstrated its use by quantifying the essentialome in different strains through CRISPRi-seq, and used it to identify genes that modulate susceptibility to the lipoglycopeptide dalbavancin. By exposing the library to sublethal concentrations of dalbavancin using both CRISPRi-seq and direct selection methods, we found genes previously reported to be involved in antibiotic susceptibility, but also identified genes thus far unknown to affect antibiotic tolerance. Importantly, some of these genes could not have been detected by more conventional knock-out approaches because they are essential for growth, stressing the complementary value of CRISPRi-based methods. Notably, knockdown of a gene encoding the uncharacterized protein KapB specifically sensitizes the cells to dalbavancin, but not to other antibiotics of the same class, while knockdown of the Shikimate pathway surprisingly has the opposite effect. The results presented here demonstrate the potential of CRISPRi-seq screens to identify genes and pathways involved in antibiotic susceptibility and pave the way to explore alternative antimicrobial treatments through these insights.
VCP increases or decreases tau seeding using specific cofactors
Authors: Batra Sushobhna , Vaquer-Alicea Jaime , Manon Victor A. , Kashmer Omar M. , Lemoff Andrew , Cairns Nigel J. , White Charles L. , Diamond Marc I. 
Published: September 2023

AbstractBackgroundNeurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm.In vitroseeding reactions typically take days, yet seeding into the complex cytoplasmic milieu can happen within hours. A cellular machinery might regulate this process, but potential players are unknown.MethodsWe used proximity labeling to identify factors that control seed amplification. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity upon seeded intracellular tau aggregation. We identified valosin containing protein (VCP/p97) 5h after seeding. Mutations in VCP underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We utilized tau biosensors, a cellular model for tau aggregation, to study the effects of VCP on tau seeding.ResultsVCP knockdown reduced tau seeding. However, distinct chemical inhibitors of VCP and the proteasome had opposing effects on aggregation, but only when given <8h of seed exposure. ML-240 increased seeding efficiency ∼40x, whereas NMS-873 decreased seeding efficiency by 50%, and MG132 increased seeding ∼10x. We screened VCP co-factors in HEK293 biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. Reduction of FAF2 and UBXN6 increased tau seeding.ConclusionsVCP uses distinct cofactors to determine seed replication efficiency, consistent with a dedicated cytoplasmic processing complex that directs seeds towards dissolution vs. amplification.
Genome-wide screens reveal shared and strain-specific genes that facilitate enteric colonization byKlebsiella pneumoniae
Authors: Cheung Bettina H , Alisoltani Arghavan , Kochan Travis J , Lebrun-Corbin Marine , Nozick Sophia H , Axline Christopher MR , Bachta Kelly ER , Ozer Egon A , Hauser Alan R 
Published: September 2023

ABSTRACTGastrointestinal (GI) colonization byKlebsiella pneumoniaeis a risk factor for subsequent infection as well as transmission to other patients. Additionally, colonization is achieved by many strain types that exhibit high diversity in genetic content. Thus, we aimed to study strain-specific requirements forK. pneumoniaeGI colonization by applying transposon insertion sequencing to three classical clinical strains: a carbapenem-resistant strain, an extended-spectrum beta-lactamase producing strain, and a non-epidemic antibiotic-susceptible strain. The transposon insertion libraries were screened in a murine model of GI colonization. At three days post-inoculation, 27 genes were required by all three strains for colonization. Isogenic deletion mutants for three genes/operons (acrA,carAB,tatABCD) confirmed colonization defects in each of the three strains. Additionally, deletion ofacrAreduced bile tolerancein vitro, while complementation restored both bile tolerancein vitroand colonization abilityin vivo. Transposon insertion sequencing suggested that some genes were more important for colonization of one strain than the others. For example, deletion of the sucrose porin-encoding genescrYresulted in a colonization defect in the carbapenemase-producing strain but not in the extended-spectrum beta-lactamase producer or the antibiotic-susceptible strain. These findings demonstrate that classicalK. pneumoniaestrains use both shared and strain-specific strategies to colonize the mouse GI tract.IMPORTANCEKlebsiella pneumoniaeis a common cause of difficult-to-treat infections due to its propensity to express resistance to many antibiotics. For example, carbapenem-resistantK. pneumoniae(CR-Kp) has been named an urgent threat by the United States Centers for Disease Control and Prevention. Gastrointestinal colonization of patients withK. pneumoniaehas been linked to subsequent infection, making it a key process to control in prevention of multidrug-resistant infections. However, the bacterial factors which contribute toK. pneumoniaecolonization are not well understood. Additionally, individual strains exhibit large amounts of genetic diversity, begging the question of whether some colonization factors are strain-dependent. This study identifies the enteric colonization factors of 3 classical strains using transposon mutant screens to define a core colonization program forK. pneumoniaeas well as detecting strain-to-strain differences in colonization strategies.
Ras-mediated homeostatic control of front-back signaling dictates cell polarity
Authors: Lin Yiyan , Pal Dhiman Sankar , Banerjee Parijat , Banerjee Tatsat , Qin Guanghui , Deng Yu , Borleis Jane , Iglesias Pablo A. , Devreotes Peter N. 
Published: September 2023

AbstractStudies in the model systems,Dictyosteliumamoebae and HL-60 neutrophils, have shown that local Ras activity directly regulates cell motility or polarity. Localized Ras activation on the membrane is spatiotemporally regulated by its activators, RasGEFs, and inhibitors, RasGAPs, which might be expected to create a stable ‘front’ and ‘back’, respectively, in migrating cells. Focusing on C2GAPB in amoebae and RASAL3 in neutrophils, we investigated how Ras activity along the cortex controls polarity. Since existing gene knockout and overexpression studies can be circumvented, we chose optogenetic approaches to assess the immediate, local effects of these Ras regulators on the cell cortex. In both cellular systems, optically targeting the respective RasGAPs to the cell front extinguished existing protrusions and changed the direction of migration, as might be expected. However, when the expression of C2GAPB was induced globally, amoebae polarized within hours. Furthermore, within minutes of globally recruiting either C2GAPB in amoebae or RASAL3 in neutrophils, each cell type polarized and moved more rapidly. Targeting the RasGAPs to the cell backs exaggerated these effects on migration and polarity. Overall, in both cell types, RasGAP-mediated polarization was brought about by increased actomyosin contractility at the back and sustained, localized F-actin polymerization at the front. These experimental results were accurately captured by computational simulations in which Ras levels control front and back feedback loops. The discovery that context-dependent Ras activity on the cell cortex has counterintuitive, unanticipated effects on cell polarity can have important implications for future drug-design strategies targeting oncogenic Ras.
Effect of cannabigerol on sleep and quality of life in Veterans: A decentralized, randomized, placebo-controlled trial
Authors: Emerson Chris R , Webster Courtney E , Daza Eric J , Klamer Brett G , Tummalacherla Meghasyam 
Published: September 2023

AbstractBackground/ObjectiveThis decentralized, randomized, triple-blind, placebo-controlled study evaluated the efficacy and safety of an oral cannabigerol (CBG) formulation in Veterans with sleep issues.MethodsAfter inclusion, randomization and a two-week run-in phase, participants received CBG (25 mg daily for two weeks, escalated to 50 mg daily for a further two weeks) or placebo. The primary endpoint was change in sleep quality, assessed via the Medical Outcomes Study Sleep Problems Index II (MOS-SS SPI-II). Additional endpoints included change in quality of life (WHODAS-2.0–12), post-traumatic stress disorder symptoms (PCL-5) and sleep actigraphy data. Safety was assessed based on adverse event reporting.ResultsA total of 63 participants were randomized to receive CBG (n=33) or placebo (n=30) and formed the intention-to-treat (ITT) population. Of these, 35 completed the study without major protocol deviations (CBG [n=18]; placebo [n=17]) and formed the per-protocol (PP) population. During active treatment (between day 14 and day 42) MOS-SS SPI-II scores declined numerically (indicating improved sleep) in both treatment groups (in both the ITT and the PP populations) with no statistically discernible difference between the CBG and placebo groups. Similar patterns were observed for WHODAS-2.0–12 and PCL-5 scores. Actigraphy data indicated no discernible difference in sleep patterns between the treatment groups. Five mild, nonserious, adverse events were reported with CBG.ConclusionsBoth CBG and placebo tended towards sleep and QoL improvement in Veterans. While no firm conclusion on the efficacy of CBG in improving sleep can be made, the favorable safety profile supports future studies to investigate the benefit of CBG.
Clinical evaluation of deep learning-based risk profiling in breast cancer histopathology and comparison to an established multigene assay
Authors: Wang Yinxi , Sun Wenwen , Karlsson Emelie , Lövgren Sandy Kang , Ács Balázs , Rantalainen Mattias , Robertson Stephanie , Hartman Johan 
Published: September 2023

ABSTRACTA significant proportion of oestrogen receptor (ER)-positive and human epidermal growth factor receptor 2 (HER2)-negative early breast cancer patients are categorised as intermediate risk based on classic clinicopathological variables, thus providing limited information to guide treatment decisions. The Prosigna assay is one of the established prognostic multigene assays in clinical practice for risk profiling. Stratipath Breast is a novel deep learning-based image analysis tool that utilises haematoxylin and eosin (HE)-stained histopathological images for risk profiling. In this study, we aimed to evaluate the Stratipath Breast tool for image-based risk profiling and compare it with the Prosigna assay. In a real-world breast cancer case series comprising 234 invasive tumours from patients with early ER+/HER2-breast cancer, clinically intermediate risk and eligible for chemotherapy, clinicopathological data including Prosigna results and corresponding HE-stained tissue slides were retrieved. The digitised HE slides were analysed by Stratipath Breast. Our findings showed that the Stratipath Breast analysis identified 49.6% of the clinically intermediate tumours as low risk and 50.4% as high risk. The Prosigna assay classified 32.5%, 47.0% and 20.5% tumours as low, intermediate and high risk, respectively. Among Prosigna intermediate-risk tumours, 47.3% were stratified as Stratipath low risk and 52.7% as high risk. In addition, 89.7% of Stratipath low-risk cases were classified as Prosigna low/intermediate risk. The overall agreement between the two tests for low-risk and high-risk groups was 71.0%, with a Cohen’s kappa of 0.42. For both risk profiling tests, grade and Ki67 differed significantly between risk groups. In conclusion, for the first time, we here present the results from a clinical evaluation of image-based risk stratification and show a considerable agreement to an established gene expression assay in routine breast pathology. The findings demonstrate that image-based risk profiling may aid in the identification of low-risk patients who could potentially be spared adjuvant chemotherapy.
Antiviral activity of intracellular nanobodies targeting the influenza virus RNA-polymerase core
Authors: Bessonne Mélissa , Morel Jessica , Nevers Quentin , Ballandras-Colas Allison , Grange Magali , Roussel Alain , Crépin Thibaut , Delmas Bernard 
Published: September 2023

AbstractInfluenza viruses transcribe and replicate their genome in the nucleus of the infected cells, two functions that are supported by the viral RNA-dependent RNA-polymerase (FluPol). FluPol displays structural flexibility related to distinct functional states, from an inactive form to conformations competent for replication and transcription. FluPol machinery is constituted by a structurally-invariant core comprising the PB1 subunit stabilized with PA and PB2 domains, whereas the PA endonuclease and PB2 C-domains can pack in different configurations around the core. To get insights into the functioning of FluPol, we selected single-domain nanobodies (VHHs) specific of the influenza A FluPol core. When expressed intracellularly, several of them exhibited inhibitory activity on type A FluPol, but not on the type B one. The most potent VHH (VHH16) targets PA, but preferentially bind the PA-PB1 dimer with an affinity below the nanomolar range. Ectopic intracellular expression of VHH16 in virus permissive cells blocks multiplication of different influenza A subtypes, even when induced at late times post-infection. VHH16 was found to impair the transport of the PA-PB1 dimer to the nucleus, without affecting its handling by the importin β RanBP5 and subsequent steps in FluPol assembly. These data suggest that the VHH16 neutralization activity is likely due to an alteration of the import of the PA-PB1 dimer into the nucleus, resulting to an inhibition of FluPol functioning. VHH16 binding site represent a potential target for antiviral development.Author SummaryThe influenza virus RNA-polymerase (FluPol) ensures genome transcription and replication in the nucleus of the infected cells. To select ligands able to block FluPol activities, we screened a library of phages encoding nanobodies and resulting from the immunization of a llama with FluPol subunits. When expressed intracellularly, one of the nanobodies displays highly efficient FluPol blocking and virus neutralizing activities. This nanobody binds FluPol with high affinity and recognizes preferentially the PA-PB1 assembled subunits. Furthermore, it was found to interfere with the transport of the PA-PB1 dimer into the nucleus, suggesting that targeting FluPol trafficking between the cytoplasm and the nucleus may constitute a powerful strategy to develop new antivirals.