bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifiability analysis and noninvasive online estimation of the first-order neural activation dynamics in the brain with closed-loop transcranial magnetic stimulation
Authors: Alavi Seyed Mohammad Mahdi , Mahdi Adam , Vila-Rodriguez Fidel , Goetz Stefan M 
Published: July 2022

AbstractBackgroundNeurons demonstrate very distinct nonlinear activation dynamics, influenced by the neuron type, morphology, ion channel expression, and various other factors. The measurement of the activation dynamics can identify the neural target of stimulation and detect deviations, e.g., for diagnosis. This paper describes a tool for closed-loop sequential parameter estimation (SPE) of the activation dynamics through transcranial magnetic stimulation (TMS). The proposed SPE method operates in real time, selects ideal stimulus parameters, detects and processes the response, and concurrently estimates the input–output (IO) curve and the first-order approximation of the activated neural target.ObjectiveTo develop a method for concurrent SPE of the first-order activation dynamics and IO curve with closed-loop TMS.MethodFirst, identifiability of an integrated model of the first-order neural activation dynamics and IO curve is assessed, demonstrating that at least two IO curves need to be acquired with different pulse widths. Then, a two-stage SPE method is proposed. It estimates the IO curve by using Fisher information matrix (FIM) optimization in the first stage and subsequently estimates the membrane time constant as well as the coupling gain in the second stage. The procedure continues in a sequential manner until a stopping rule is satisfied.ResultsThe results of 73 simulation cases confirm the satisfactory estimation of the membrane time constant and coupling gain with average absolute relative errors (AREs) of 6.2% and 5.3%, respectively, with an average of 344 pulses (172 pulses for each IO curve or pulse width). The method estimates the IO curves’ lower and upper plateaus, mid-point, and slope with average AREs of 0.2%, 0.7%, 0.9%, and 14.5%, respectively. The conventional time constant estimation method based on the strength-duration (S–D) curve leads to 33.3% ARE, which is 27.0% larger than 6.2% ARE obtained through the proposed real-time FIM-based SPE method in this paper.ConclusionsSPE of the activation dynamics requires acquiring at least two IO curves with different pulse widths, which needs a controllable TMS (cTMS) device with adjustable pulse duration.SignificanceThe proposed SPE method enhances the cTMS functionality, which can contribute novel insights in research and clinical studies.
DeepInsight-3D for precision oncology: an improved anti-cancer drug response prediction from high-dimensional multi-omics data with convolutional neural networks
Authors: Sharma Alok , Lysenko Artem , Boroevich Keith A , Tsunoda Tatsuhiko 
Published: July 2022

AbstractModern oncology offers a wide range of treatments and therefore choosing the best option for particular patient is very important for optimal outcomes. Multi-omics profiling in combination with AI-based predictive models have great potential for streamlining these treatment decisions. However, these encouraging developments continue to be hampered by very high dimensionality of the datasets in combination with insufficiently large numbers of annotated samples. In this study, we propose a novel deep learning-based method to predict patient-specific anticancer drug response from three types of multiomics data. The proposed DeepInsight-3D approach relies on structured data-to-image conversion that then allows use of convolutional neural networks, which are particularly robust to high dimensionality of the inputs while retaining capabilities to model highly complex relationships between variables. Of particular note, we demonstrate that in this formalism additional channels of an image can be effectively used to accommodate data from different ‘omics layers while explicitly encoding the connection between them. DeepInsight-3D was able to outperform two other state-of-the-art methods proposed for this task. These advances can facilitate the development of better personalized treatment strategies for different cancers in the future.
Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology
Authors: MacDonald Samual , Foley Helena , Yap Melvyn , Johnston Rebecca L. , Steven Kaiah , Koufariotis Lambros T. , Sharma Somwya , Wood Scott , Addala Venkateswar , Pearson John V. , Roosta Fred , Waddell Nicola , Kondrashova Olga , Trzaskowski Maciej 
Published: July 2022

AbstractTrust and transparency are critical for deploying deep learning (DL) models into the clinic. DL application poses generalisation obstacles since training/development datasets often have different data distributions to clinical/production datasets that can lead to incorrect predictions with underestimated uncertainty. To investigate this pitfall, we benchmarked one pointwise and three approximate Bayesian DL models used to predict cancer of unknown primary with three independent RNA-seq datasets covering 10,968 samples across 57 primary cancer types. Our results highlight simple and scalable Bayesian DL significantly improves the generalisation of uncertainty estimation (e.g., p-value = 0.0013 for calibration). Moreover, we demonstrate Bayesian DL substantially improves accuracy under data distributional shifts when utilising ‘uncertainty thresholding’ by designing a prototypical metric that evaluates the expected (accuracy) loss when deploying models from development to production, which we call the Area between Development and Production curve (ADP). In summary, Bayesian DL is a hopeful avenue of research for generalising uncertainty, which improves performance, transparency, and therefore safety of DL models for deployment in real-world.
Rapid protein stability prediction using deep learning representations
Authors: Blaabjerg Lasse M. , Kassem Maher M. , Good Lydia L. , Jonsson Nicolas , Cagiada Matteo , Johansson Kristoffer E. , Boomsma Wouter , Stein Amelie , Lindorff-Larsen Kresten 
Published: July 2022

AbstractPredicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, and when elucidating the molecular mechanisms behind evolution and disease. Here, we present RaSP, a method for making rapid and accurate predictions of changes in protein stability by leveraging deep learning representations. RaSP performs on-par with biophysics-based methods and enables saturation mutagenesis stability predictions in less than a second per residue. We use RaSP to calculate ∼ 300 million stability changes for nearly all single amino acid changes in the human proteome, and examine variants observed in the human population. We find that variants that are common in the population are substantially depleted for severe destabilization, and that there are substantial differences between benign and pathogenic variants, highlighting the role of protein stability in genetic diseases. RaSP is freely available—including via a Web interface—and enables large-scale analyses of stability in experimental and predicted protein structures.
A role for brassinosteroid signaling in decision-making processes in the Arabidopsis seedling
Authors: Kalbfuß Nils , Strohmayr Alexander , Kegel Marcel , Le Lien , Grosseholz Friederike , Brunschweiger Barbara , Stöckl Katharina , Wiese Christian , Franke Carina , Schiestl Caroline , Prem Sophia , Sha Shuyao , Franz-Oberdorf Katrin , Hafermann Juliane , Thiemé Marc , Facher Eva , Palubicki Wojciech , Bolle Cordelia , Assaad Farhah F. 
Published: July 2022

SUMMARYPlants often adapt to adverse conditions via differential growth, whereby limited resources are discriminately allocated to optimize the growth of one organ at the expense of another. Little is known about the decision-making processes that underly differential growth. In this study, we developed a screen to identify decision making mutants by deploying two tools that have been used in decision theory: a well-defined yet limited budget, as well as conflict-of-interest scenarios. A forward genetic screen that combined light and water withdrawal was carried out. This identified BRASSINOSTEROID INSENSITIVE 2 (BIN2) alleles as decision mutants with “confused” phenotypes. An assessment of organ and cell length suggested that hypocotyl elongation occurred predominantly via cellular elongation. In contrast, root growth appeared to be regulated by a combination of cell division and cell elongation or exit from the meristem. Brassinosteroid signalling mutants were most severely impaired in their ability to adjust cell geometry in the hypocotyl and cell elongation as a function of distance from the quiescent centre in the root tips. This study describes a novel paradigm for root growth under limiting conditions, which depends not only on hypocotyl-versus-root trade-offs in the allocation of limited resources, but also on an ability to deploy different strategies for root growth in response to multiple stress conditions.
Rare Ribosomal RNA Sequences from Archaea Stabilize the Bacterial Ribosome
Authors: Nissley Amos J. , Penev Petar I. , Watson Zoe L. , Banfield Jillian F. , Cate Jamie H. D. 
Published: July 2022

ABSTRACTRibosomes serve as the universally conserved translators of the genetic code into proteins and must support life across temperatures ranging from below freezing to above the boiling point of water. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Peptide bond formation by the ribosome requires correct positioning of the 3’
s-end of the aminoacylated tRNA (aa-tRNA) substrate, which is aided by an RNA hairpin in the ribosomal RNA (rRNA) of the large subunit, termed the A loop. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3′-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not exert a dominant negative effect on cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation in the peptidyl transferase center of the archaeal ribosome that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.
Antibiotic-tolerant persisters are pervasive among clinical Streptococcus pneumoniae isolates and show strong condition-dependence
Authors: Geerts Nele , De Vooght Linda , Passaris Ioannis , Van den Bergh Bram , Cos Paul 
Published: July 2022

ABSTRACTStreptococcus pneumoniae is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in S. pneumoniae is an emerging problem as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet, in S. pneumoniae nothing is known about antibiotic-tolerant persisters. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. Here, we set out to identify and characterize persistence in S. pneumoniae. Specifically, we followed different strategies to overcome the self-limiting nature of S. pneumoniae as confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. In optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of S. pneumoniae clinical isolates, which shows that a high natural diversity in persistence is widely present in S. pneumoniae. Collectively, this proof-of-concept significantly progresses the understanding of the importance of antibiotic persistence in S. pneumoniae infections which will set stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research.IMPORTANCES. pneumoniae is considered a serious threat by the Centers of Disease Control and Prevention through arising antibiotic resistance. In addition to resistance, bacteria can also survive lethal antibiotic treatment by developing antibiotic tolerance and more specifically by antibiotic tolerance through persistence. This phenotypic variation seems omnipresent among bacterial life, is linked to therapy failure and acts as a catalyst for resistance development. This study gives the first proof of the presence of persister cells in S. pneumoniae and shows a high variety in persistence levels among diverse strains, suggesting persistence is a general trait in S. pneumoniae cultures and that a broad range of genetic elements are controlling the phenotype. Together, our work advocates for higher interest for persistence in S. pneumoniae as a contributing factor for therapy failure and resistance development.
The difference in FRET efficiency fluctuation at each end of the actin filament
Authors: Mitani Takahiro , Mashiko Ryota , Nezasa Miku , Nishikata Ichiro , Kamimura Kenji , Honda Hajime , Fujiwara Ikuko 
Published: July 2022

AbstractActin filaments are involved in various cell motility processes. Actin polymerisation is primarily governed by monomer association and dissociation occurring at the rapid-growing end called the barbed end, which generates the force to push the plasma membrane forward. Individual actin filaments bind to one nucleotide and its hydrolysis energy is used to maintain the filamentous form by changing the characteristics of the subunits. The asymmetry of the individual actin filaments is also important for detecting the asymmetry of the cell. However, asymmetry at the subunit level including conformational and temporal changes in actin filaments has not been visualized yet. Here, we used “Förster (or fluorescence) resonance energy transfer (FRET)-actin filament” by copolymerising an equal amount of donor and acceptor labelled actin. FRET efficiency change was measured along each actin filament under a light microscope. The FRET efficiency was lower near the end region than in the interior regions. Fluctuations in the FRET efficiency (fFRET) were used to monitor local flexibilities along each actin filament. The fFRET was larger near the end region than the interior region. Our quantified data showed that spatial change of fFRET along actin filaments was rapidly decayed from the barbed end from near the pointed end toward internal region, suggesting that the behaviour of actin subunits near ends is affected from each end. Our result revealed that actin filaments have different orientations locally. These orientations appear when actin forms filaments, which may contribute the cell motility.
Regulated Degradation of the Inner Nuclear Membrane Protein SUN2 Maintains Nuclear Envelope Architecture and Function
Authors: Krshnan Logesvaran , Siu Wingyan Skyla , Van de Weijer Michael , Hayward Daniel , Guerrero Elena Navarro , Gruneberg Ulrike , Carvalho Pedro 
Published: July 2022

AbstractNuclear architecture and functions depend on dynamic interactions between nuclear components (such as chromatin) and inner nuclear membrane (INM) proteins. Mutations in INM proteins interfering with these interactions result in disease. However, mechanisms controlling the levels and turnover of INM proteins remain unknown. Here, we describe a mechanism of regulated degradation of the INM SUN domain-containing protein 2 (SUN2). We show that Casein Kinase II and the C-terminal domain Nuclear Envelope Phosphatase 1 (CTDNEP1) have opposing effects on SUN2 levels by regulating SUN2 binding to the ubiquitin ligase Skp/Cullin1/F-BoxβTrCP(SCFβTrCP). Upon binding to phosphorylated SUN2, SCFβTrCPpromotes its ubiquitination. Ubiquitinated SUN2 is membrane extracted by the AAA ATPase p97 and delivered to the proteasome for degradation. Importantly, accumulation of non-degradable SUN2 results in aberrant nuclear architecture, vulnerability to DNA damage and increased lagging chromosomes in mitosis. These findings uncover a central role of proteolysis in INM protein homeostasis.
Immunological contributions to age-dependent variations in behavioural responses to cutaneous inflammation
Authors: Dayman Emma , Bennett Andrew , Hathway Gareth J. 
Published: July 2022

AbstractSystemic responses to immune challenge are immature at birth. However exposure to experimental inflammogens are able to produce an immunologic response which is characterised by swelling and oedema but, unlike in adults, does not result in sensory hypersensitivity. We sought to investigate whether the lack of nociceptive hypersensitivity was as a result of altered hemapoietic immune cell recruitment to the site of inflammation and/or differences in the cytokine and chemokine profile released by tissue invading cells. Postnatal (day of birth) and young adult (40-days old) Sprague-Dawley rats were used. Inflammation was induced by s.c. injection of Complete Freunds Adjuvant (CFA) unilaterally into the one hind paw. Mechanical withdrawal thresholds were measured before and after injection (2-168hrs). In adults a significant hyperalgesia was evoked which was absent in neonates. Immunohistochemical analysis of invading immune cells present in the perfusion fixed skin showed that although total cell numbers in the paw were the same in both age groups, neonates recruited more cells positive for both cell surface markers CD68 and Mannose-receptor (MR) whereas adults recruited significantly more cells positive for MR alone. There were no differences in neutrophil recruitment (as measured with H&E staining). TaqMan qPCR demonstrated that the temporal profile of cytokine production in the skin differed between ages with neonates responding faster than adults and that neonates produced significantly more IL-1b and IL-27 then adults who expressed significantly more IL-6 and IL-10. This study illustrates that in neonates the cell recruitment and cytokine profiles are markedly different to those seen in adults; this may in part explain why behavioural responses to inflammation are suppressed relative to adults.
Whole exome sequencing study identifies candidate loss of function variants and locus heterogeneity in familial cholesteatoma
Authors: Cardenas Ryan , Prinsley Peter , Philpott Carl , Bhutta Mahmood F , Wilson Emma , Brewer Daniel S. , Jennings Barbara A. 
Published: July 2022

AbstractCholesteatoma is a rare progressive disease of the middle ear. Most cases are sporadic, but some patients report a positive family history. Identifying functionally important gene variants associated with this disease has the potential to uncover the molecular basis of cholesteatoma pathology with implications for disease prevention, surveillance, or management.We performed an observational WES study of 21 individuals treated for cholesteatoma who were recruited from ten multiply affected families. These family studies were complemented with gene-level mutational burden analysis. We also applied functional enrichment analyses to identify shared properties and pathways for candidate genes and their products.Filtered data collected from pairs and trios of participants within the ten families revealed 398 rare, loss of function (LOF) variants co-segregating with cholesteatoma in 389 genes. We identified six genesDENND2C, DNAH7, NBEAL1, NEB, PRRC2C, andSHC2, for which we found LOF variants in two or more families. The parallel gene-level of mutation-burden identified a significant mutation burden for the genes in theDNAHgene family, which encode products involved in ciliary structure. Functional enrichment analyses identified common pathways for the candidate genes which included GTPase regulator activity, calcium ion binding, and degradation of the extracellular matrix.The number of candidate genes identified and the locus heterogeneity that we describe within and between multiply affected families suggest that the genetic architecture for familial cholesteatoma is complex.
Differentiating interactions of antimicrobials with Gram-negative and Gram-positive bacterial cell walls using molecular dynamics simulations
Authors: Vaiwala Rakesh , Sharma Pradyumn , Ayappa K. Ganapathy 
Published: July 2022

AbstractDeveloping molecular models to capture the complex physicochemical architecture of the bacterial cell wall and to study the interaction with antibacterial molecules is an important aspect of assessing and developing novel antimicrobial molecules. We carried out molecular dynamics simulations using an atomistic model of peptidoglycan (PGN) to represent the architecture for Gram-positive Staphylococcus aureus. The model is developed to capture various structural features of the staphylococcal cell wall, such as the peptide orientation, area per disaccharide, glycan length distribution, crosslinking, and pore size. A comparison of the cell wall density and electrostatic potentials is made with a previously developed cell wall model of Gram-negative bacteria, Escherichia coli, and properties for both a single and multilayered structures of the Staphylococcal cell wall are studied. We investigated the interactions of the antimicrobial peptide melittin with the PGN structures. The depth of melittin binding to PGN is more pronounced in E. coli than S. aureus, and consequently the melittin has greater contacts with glycan units of E. coli. Contacts of melittin with the amino acids of peptidoglycan are comparable across both the strains, and the D-Ala residues, which are sites for transpeptidation, show enhanced interactions with melittin. A low energetic barrier is observed for translocation thymol with the four-layered peptidoglycan model. The molecular model developed for Gram-positive PGN allows us to compare and contrast the cell wall penetrating properties with Gram-negative strains and assess for the first time binding and translocation of antimicrobial molecules for Gram-positive cell walls.