bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of low numbers of bacterial cells in pharmaceutical drug product using Raman Spectroscopy and PLS-DA multivariate analysis
Authors: Grosso R.A. , Walther A.R. , Brunbech E. , Sørensen A. , Schebye B. , Olsen K.E. , Qu H. , Hedegaard M.A.B. , Arnspang E. C. 
Published: May 2022

AbstractSterility testing is a laborious and slow process to detect contaminants present in drug products. Raman spectroscopy is a promising label-free tool to detect microorganisms and thus gaining relevance as future alternative culture-free method for sterility testing in pharmaceutical industry. However, reaching detection limits similar to standard procedures while keeping a high accuracy remains challenging, due to weak bacterial Raman signal. In this work, we show a new non-invasive approach focusing on detect different bacteria in concentrations below 100 CFU/ml within drug product containers using Raman spectroscopy and multivariate data analysis. Even though Raman spectra form drug product with and without bacteria are similar, a partial least squared discriminant analysis (PLS-DA) model shows great performance to distinguish samples with bacteria contaminants in limits below 10 CFU/ml. We use spiked samples with bacteria spores for independent validation achieving a detection accuracy of 99%. Our results indicate a great potential of this rapid, and cost-effective approach to be use in quality control of pharmaceutical industry.
The EGFR-STYK1-FGF1 axis sustains functional drug tolerance to EGFR inhibitors in EGFR-mutant non-small cell lung cancer
Authors: Eggermont Carolien , Giron Philippe , Noeparast Maxim , Vandenplas Hugo , Aza-Blanc Pedro , Gutierrez Gustavo J. , De Grève Jacques 
Published: May 2022

AbstractNon-small cell lung cancer (NSCLC) patients harboring activating mutations in epidermal growth factor receptor (EGFR) are sensitive to therapy with EGFR tyrosine kinase inhibitors (TKI). Despite remarkable clinical responses using EGFR TKI, surviving drug tolerant cells serve as a reservoir from which drug resistant tumors may emerge. This study addresses the need for improved efficacy of EGFR TKI by identifying targets involved in functional drug tolerance against them. To this aim, a high-throughput siRNA kinome screen was performed using two EGFR TKI-sensitive EGFR-mutant NSCLC cell lines in the presence/absence of the second-generation EGFR TKI afatinib. From the screen, Serine/Threonine/Tyrosine Kinase 1 (STYK1) was identified as a target that when downregulated potentiates the effects of EGFR inhibitionin vitro. We found that chemical inhibition of EGFR combined with the siRNA-mediated knockdown of STYK1 led to a significant decrease in cancer cell viability and anchorage-independent cell growth. Further, we show that STYK1 selectively interacts with mutant EGFR and that the interaction is disrupted upon EGFR inhibition. Finally, we identified fibroblast growth factor 1 (FGF1) as a downstream effector of STYK1 in NSCLC cells. Accordingly, downregulation of STYK1 counteracted the afatinib-induced upregulation of FGF1. Altogether, we unveil STYK1 as a valuable target to repress the pool of surviving drug tolerant cells arising upon EGFR inhibition. Co-targeting of EGFR and STYK1 could lead to a better overall outcome for NSCLC patients.
2,4-Diacetylphloroglucinol Against Candida albicans: Biofilm Formation, Aspartyl Protease Production and Ultrastructure Changes
Authors: Stepanov Artyom A. , Vasilchenko Alexey S. 
Published: May 2022

AbstractThe dimorphic fungus Candida albicans is the one of the most important opportunistic pathogen of human. The use of fungicides against candida encounters sub-inhibitory effects, which are fungal stress response and undesirable for the host. In this work we investigated antifungal action of 2,4-diacetylphloroglucinol against Candida albicans ATCC 10231 with focus on they biofilm forming ability under the treatment.It was found that 2,4-DAPG reduced ability of candida cells to form biofilm, but complete inhibition or irradiation did not achieve. Moreover, Candida albicans cells in the adherent state have been characterized by reduced susceptibility to 2,4-DAPG comparing to planktonic cells.Investigation of mechanisms which could be explain the antibiofilm action of 2,4-DAPG has revealed the reduction in cell’s surface hydrophobicity and inhibition of yeast-to-hyphae transition. Biofilms formed under the sub-inhibitory concentrations of 2,4-DAPG were depleted in protein and carbohydrate content. Furthermore, we microscopically visualized the treated biofilms and have revealed numerous cannels localized on hyphae and associated with secretion of aspartyl proteases (Sap).We assumed what excretion of Sap is triggered by reactive oxygen generated upon affecting of mitochondrion respiration by 2,4-DAPG. Introducing of antioxidant Trolox simultaneously with 2,4-DAPG lead to reducing of Sap production. Thus, production of aspartyl proteases is a one of undesirable side effect of Candida albicans treatment, but using 2,4-DAPG in combination with antioxidants is the solution to overcome it.
Cancer stem cell-derived extracellular vesicles preferentially target MHC-II– macrophages and PD1+ T cells in the tumor microenvironment
Authors: Gonzalez-Callejo P. , Guo Z. , Ziglari T. , Claudio N.M. , Oshimori N. , Seras-Franzoso J. , Pucci F. 
Published: May 2022

AbstractImmunotherapy is an approved treatment option for head and neck squamous cell carcinoma (HNSCC). However, the response rate to immune checkpoint blockade is only 13% for recurrent HNSCC, highlighting the urgent need to better understand tumor-immune interplay, with the ultimate goal of improving patient outcomes. HNSCC present high local recurrence rates and therapy resistance that can be attributed to the presence of cancer stem cells (CSC) within tumors. CSC exhibit singular properties that enable them to avoid immune detection and eradication. The immune cell types that directly engage with CSC to allow immune escape and cancer recurrence are still unknown. Here, we genetically engineered CSC-derived extracellular vesicles (EVs) to perform sortase-mediated in vivo proximity labeling. We identified specific immune cell subsets recruited into the CSC niche. We demonstrated that unmanipulated CSC-EVs preferentially target MHC-II– macrophages and PD1+ T cells, and that such EV-mediated intercellular communication between CSC and these immune cells contributed to the observed spatial interactions and niche sharing. These results suggest that combination therapies targeting CSC, tumor macrophages and PD1 may synergize and lower local recurrence rates in HNSCC patients.
Lhx9 haploinsufficiency alters transcription in the adult mouse ovary, causing subfertility and abnormal epithelium
Authors: Workman Stephanie , Wilson Megan J. 
Published: May 2022

AbstractUnderstanding the molecular pathways that underpin ovarian development and function is vital for improving the research approaches to investigating fertility. Despite a significant improvement in our knowledge of molecular activity in the ovary, many questions remain unanswered in the quest to understand factors influencing fertility and ovarian pathologies such as cancer. Here we present an investigation into the expression and function of developmental transcription factor LIM Homeobox 9 (LHX9) in the adult mouse ovary. We have characterised Lhx9 expression in several cell types of the mature ovary across follicle stages. To elucidate the function of this expression, we carried out an investigation of ovarian anatomy and transcription in a Lhx9+/- knockout mouse model displaying subfertility. Despite a lack of gross anatomical differences between genotypes, RNA-sequencing found that 90 genes were differentially expressed between Lhx9+/- and Lhx9+/+ mice. Gene ontology analyses revealed a downregulation of genes with major roles in ovarian steroidogenesis and an upregulation of genes with implications for ovarian cancer. Analysis of the ovarian epithelium revealed Lhx9+/- mice have a disorganised epithelial phenotype and a significant increase in epithelial marker gene expression. These results provide an analysis of Lhx9 in the adult mouse ovary and a new candidate for fertility research and ovarian epithelial cancer.Summary sentenceLhx9 haploinsufficient mice are subfertile with altered expression of steroid genes in the adult ovary and abnormal ovarian surface epithelium.
Hemodynamic transient and functional connectivity follow structural connectivity and cell type over the brain hierarchy
Authors: Chuang Kai-Hsiang , Huang Helena H , Gerdekoohi Shabnam Khorasani , Li Zengmin , Athwal Dilsher 
Published: May 2022

AbstractThe neural circuit of the brain is organized as a hierarchy of functional units with wide-ranging connections that support information flow and functional connectivity. Studies using magnetic resonance imaging (MRI) indicate a moderate coupling between structural and functional connectivity at the system level. However, how do connections of different directions (feedforward and feedback) and regions with different excitatory and inhibitory (E/I) neurons shape the hemodynamic activity and functional connectivity over the hierarchy are unknown. Here, we used functional MRI to detect optogenetic-evoked and resting-state activities over a somatosensory pathway in the mouse brain in relation to axonal projection and E/I distribution. Using a highly sensitive ultrafast imaging, we identified extensive activation in regions up to the third order of axonal projections following optogenetic excitation of the ventral posteriomedial nucleus of the thalamus. The evoked response and functional connectivity correlated with feedforward projections more than feedback projections and weakened with the hierarchy. The hemodynamic response exhibited regional and hierarchical differences, with slower and more variable responses in high-order areas and bipolar response predominantly in the contralateral cortex. Importantly, the positive and negative parts of the hemodynamic response correlated with E/I neuronal densities, respectively. Furthermore, resting-state functional connectivity was more associated with E/I distribution whereas stimulus-evoked effective connectivity followed structural wiring. These findings indicate that the structure-function relationship is projection-, cell-type- and hierarchy-dependent. Hemodynamic transients could reflect E/I activity and the increased complexity of hierarchical processing.Significance StatementThe neural circuit of the brain is organized as a hierarchy of functional units with complicated feedforward and feedback connections to selectively enhance (excitation) or suppress (inhibit) information from massive sensory inputs. How brain activity is shaped by the structural wiring and excitatory and inhibitory neurons is still unclear. We characterize how brain-wide hemodynamic responses reflect these structural constituents over the hierarchy of a somatosensory pathway. We find that functional activation and connectivity correlate with feedforward connection strengths and neuronal distributions. This association subsides with hierarchy due to slower and more variable hemodynamic responses, reflecting increased complexity of processing and neuronal compositions in high-order areas. Our findings indicate that hemodynamics follow the hierarchy of structural wiring and neuronal distribution.
Molecular dynamics of spike variants in the locked conformation: RBD interfaces, fatty acid binding and furin cleavage sites
Authors: Shoemark Deborah K. , Oliveira A. Sofia F. , Davidson Andrew D. , Berger Imre , Schaffitzel Christiane , Mulholland Adrian J. 
Published: May 2022

AbstractSince December 2019 the SARS-CoV-2 virus has infected billions of people around the world and caused millions of deaths. The ability for this RNA virus to mutate has produced variants that have been responsible for waves of infections across the globe. The spike protein on the surface of the SARS-CoV-2 virion is responsible for cell entry in the infection process. Here we have studied the spike proteins from the Original, Alpha (B.1.1.7), Delta (B1.617.2), Delta-plus (B1.617.2-AY1), Omicron BA.1 and Omicron BA.2 variants. Using models built from cryo-EM structures with linoleate bound (6BZ5.pdb) and the N-terminal domain from 7JJI.pdb, each is built from the first residue, with missing loops modelled and 45 disulphides per trimer. Each spike variant was modified from the same Original model framework to maximise comparability. Three replicate, 200 ns atomistic molecular dynamics simulations were performed for each case. (These data also provide the basis for further, non-equilibrium molecular dynamics simulations, published elsewhere.) The analysis of our equilibrium molecular dynamics reveals that sequence variation at the closed receptor binding domain interface particularly for Omicron BA.2 has implications for the avidity of the locked conformation, with potential effects on Omicron BA.1 and Delta-plus. Linoleate binding has a mildly stabilizing effect on furin cleavage site motions in the Original and Alpha variants, but has no effect in Delta, Delta-plus and slightly increases motions at this site for Omicron BA.1, but not BA.2, under these simulation conditions.
The SARS-CoV-2 cellular receptor ACE2 is expressed in oropharyngeal cells and is modulated in vitro by the bacterial lysate Lantigen B
Authors: Pizzimenti Caterina , D’Agostino Antonella , Pirrello Paola , Ruiba Alessia , Melioli Giovanni 
Published: May 2022

AbstractAngiotensin-converting enzyme2 (ACE2) is the main cell surface receptor of the SARS-CoV-2 spike protein and is expressed in a variety of cell types, including cells of the respiratory tract. A bacterial lysate used for the prophylaxis of respiratory infections (OM-85), was recently shown to downregulate the expression of ACE2 in epithelial cells, suggesting its possible role as a prophylaxis of the onset of COVID19. Another bacterial lysate (Lantigen B, administered sublingually) is used in the prophylaxis of recurrent respiratory tract infections. It contains antigens obtained by chemical lysis from the most representative microbes of the respiratory tract. In this in vitro study, the capacity of Lantigen B to decrease ACE2 in human oropharyngeal cells was evaluated. The study was carried out in 40 healthy donors undergoing oropharyngeal swab for routine SARS-CoV-2 detection. Cells were treated in vitro with a 1:2 of Lantigen B. ACE2 expression was evaluated using a fluorescent anti-ACE2 monoclonal antibody and flow cytometry. A reduction in the number of positive cells was observed in 72% of the patients, while a modulation of ACE2 expression was observed in 62% of the samples. As a control, the expression of the CD54 rhinovirus receptor in the same cells was unaffected. To evaluate the functional effects of down regulation, in a subset of samples, the same oropharynx cells were incubated with Lantigen B and infected with wild-type SARS-CoV-2. After 24 hours, viral RNA, as assessed by rt-PCR, was significantly lower in samples treated with Lantigen B. In conclusion, this study demonstrates that Lantigen B, at a pharmacological dose, modulates the expression of the main SARS-CoV-2 receptor in oropharyngeal cells, and reduces viral yield. This activity could be synergistic with other approaches (vaccination and therapy) by reducing the number of potentially infected cells and thus reducing the effects of SARS-CoV-2 infection.
MegaBayesianAlphabet: Mega-scale Bayesian Regression methods for genome-wide prediction and association studies with thousands of traits
Authors: Qu Jiayi , Runcie Daniel , Cheng Hao 
Published: May 2022

ABSTRACTLarge-scale phenotype data are expected to increase the accuracy of genome-wide prediction and the power of genome-wide association analyses. However, genomic analyses of high-dimensional, highly correlated data are challenging. We developed MegaBayesianAlphabet to simultaneously analyze genetic variants underlying thousands of traits using the flexible priors of the Bayesian Alphabet family. As a demonstration, we implemented the BayesC prior in the R package MegaLMM and applied it to both simulated and real data sets. Our analyses show that the resulting model MegaBayesC can effectively use high-dimensional phenotypic data to improve the accuracy of genetic value prediction, the reliability of marker discovery, and the accuracy of marker effect size estimation in genome-wide analyses.
Evolution towards small colony variants of pandemic multidrug resistant ST131 Escherichia coli isolates from a 10-year bone infection
Authors: Li Fengyang , Lüthje Petra , Shafeeq Sulman , Ahl Marcus , Trcek Janja , Lacosta Analucia Diaz , Özenci Volkan , Ullberg Måns , Åkerlund Börje , Römling Ute 
Published: May 2022

ABSTRACTBackgroundChronic wounds are usually challenging to treat due to underlying medical conditions of the individual and as they readily become infected by microorganisms due to the failure of mechanical and physiological first line innate immune responses. We report here the characterization of host adaptation of five E. coli genomes including three E. coli ST131 genomes that occurred concomitantly with Enterococcus faecalis from a 10-year chronic wound infection after a foot fracture during the 2004 tsunami.MethodsThe five E. coli strains were characterized by various microbiological and genomic approaches. Microbiological methods were antimicrobial resistance, growth in different media and biofilm formation. Genomic methods were determination of the genome sequence by PacBio RSII and Illumina sequencing. Phylogenetic analyses and genome alterations such as single nucleotide polymorphisms, deletion and rearrangements that led to pseudogenes and chromosomal inversions were documented. Relevant selected metabolic and physiological pathways were analyzed for integrity.FindingStrains of two initially present sequence types, including the highly antimicrobial resistant ST405 clone, were subsequently replaced by isolates of the ubiquitous ST131 clone. The three E. coli ST131 strains showed a heavily host-adapted genome with a high number of pseudogenes and a large chromosomal inversion compared to ST131 reference strains. Furthermore, two of three E. coli ST131 isolates were small colony variants with its genetic basis in multiple genome alterations including pseudogenes and deletions in the pathway for heme biosynthesis. Pseudogene analysis indicated also the three ST131 strains to be mutator strains. Although enhanced capability of biofilm formation of the ST131 isolates was indicated by the agar plate assay, the a liquid culture biofilm assay did not display pronounced biofilm formation suggesting unconventional modes of biofilm formation.InterpretationST131 clone members, which originally appeared as commensal strains can cause urinary tract and blood stream infections and are ubiquitously found in the environment including waste water and in animals. ST131 strains have presumably been already acquired from the environment on occurrence of the initial foot fracture and can persist in wounds showing an outmost genome plasticity and adaptability which might causing the chronic infection. Although co-infection with E. faecalis might have supported chronicity, these findings indicate that in individuals with underlying metabolic diseases wound infection by ST131 E. coli isolates can be a health risk.FundingThis work was partially funded by ALF.
A task-general connectivity model reveals variation in convergence of cortical inputs to functional regions of the cerebellum
Authors: King Maedbh , Shahshahani Ladan , Ivry Richard , Diedrichsen Jörn 
Published: May 2022

AbstractWhile resting-state fMRI studies have provided a broad picture of the connectivity between human neocortex and cerebellum, the degree of convergence of cortical inputs onto cerebellar circuits remains unknown. Does each cerebellar region receive input from a single cortical area or convergent inputs from multiple cortical areas? Here we use task-based fMRI data to build a range of cortico-cerebellar connectivity models, each allowing for a different degree of convergence. We compared these models by their ability to predict cerebellar activity patterns for novel Task Sets. Models that allow some degree of convergence provided the best predictions, arguing for convergence of multiple cortical inputs onto single cerebellar voxels. Importantly, the degree of convergence varied across the cerebellum with the highest convergence observed in areas linked to language, working memory, and social cognition. These findings suggest important differences in the way that functional subdivisions of the cerebellum support motor and cognitive function.HighlightsModels of cortico-cerebellar connectivity are quantified using task-based fMRIConvergent rather than sparse inputs best characterize cortico-cerebellar connectivityCerebellar areas linked to cognition receive high convergence of cortical inputsModels successfully generalize to new tasks and new participants
Multi-tasking Deep Network for Tinnitus Classification and Severity Prediction from Multimodal Structural Images
Authors: Lin Chieh-Te , Ghosh Sanjay , Hinkley Leighton B. , Dale Corby L. , Souza Ana , Sabes Jennifer H. , Hess Christopher P. , Adams Meredith E. , Cheung Steven W. , Nagarajan Srikantan S. 
Published: May 2022

AbstractSubjective tinnitus is an auditory phantom perceptual disorder without an objective biomarker. Fast and efficient diagnostic tools will advance clinical practice by detecting or confirming the condition, tracking change in severity, and monitoring treatment response. Motivated by evidence of subtle anatomical or functional morphological information in magnetic resonance images (MRI) of the brain, we examined data-driven machine learning methods for joint tinnitus classification (tinnitus or no tinnitus) and tinnitus severity prediction. We propose a deep multi-task multi-modal framework for joint functionalities using structural MRI (sMRI) data. To leverage cross-information multimodal neuroimaging data, we integrated two modalities of 3-dimensional sMRI - T1 weighted (T1w) and T2 weighted (T2w) images. To explore the key components in the MR images that drove task performance, we segmented both T1w and T2w images into three different components - cerebrospinal fluid (CSF), grey matter (GM) and white matter (WM), and examined performance of each segmented image. Results demonstrate that our multimodal framework capitalizes on the information across both modalities (T1w and T2w) for the joint task of tinnitus classification and severity prediction. Our model outperforms existing learning-based and conventional methods in terms of accuracy, sensitivity, specificity, and negative predictive value.