bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Delphi study to establish a consensus definition and clinical reporting guidelines for Mesenchymal Stromal Cells
Authors: Renesme Laurent , Cobey Kelly D , Lê Maxime , Lalu Manoj M , Thébaud Bernard 
Published: June 2021

ABSTRACTIntroductionDespite being more than two decades of research, Mesenchymal Stromal Cell (MSC) treatments are still struggling to cross the translational gap. Two key issues that likely contribute to these failures are i) the lack of clear definition for MSC and ii) poor quality of reporting in MSC clinical studies. To address these issues, we propose a modified Delphi study to establish a consensus definition for MSC and clinical reporting guidelines for MSC.Methods and analysisWe will conduct a three-round international modified Delphi Survey. Findings from a recent scoping review examining how MSC are defined and reported in preclinical and clinical studies were used to draft the initial survey for round one of our Delphi. Participants will include a ‘core group’ of individuals as well as researchers whose work was captured in our scoping review. The core group will include stakeholders from different research fields including developmental biology, translational science, research methods, regulatory practices, scholarly journal editing, and industry. The first two survey rounds will be online, and the final round will take place in person. Each participant will be asked to rate their agreement on potential MSC definition characteristics and reporting items using a Likert scale. After each round, we will analyse data to determine which items have reached consensus for inclusion/exclusion, and then develop a revised questionnaire for any new items, or items that did not reach consensus.Ethics and disseminationThis study received ethical approval from the Ottawa Health Research Network Research Ethics Board. To support the dissemination of our findings, we will use an evidence-based ‘integrated knowledge translation’ approach to engage knowledge users from the inception of the research. This will allow us to develop a tailored end-of-project knowledge translation plan to support and ensure dissemination and implementation of the Delphi results.Strengths and limitations of this studyWe proposed to address the current limitations in MSC experimental and clinical research with a rigorous and methodological consensus building method (Delphi method) that will allow for structured communication on controversial issues.To support dissemination and implementation of our results, we will engage stakeholders and end-users from the inception of the project – such as patient partners – and will develop a tailored end of project knowledge translation plan (integrated knowledge translation approach) in order to overcome historical issues related to community uptake.To address the main limitations of a Delphi method (e.g., lack of participation, no in-person interaction or information exchange), we use a modified Delphi survey with a Core group of stakeholders and a face-to-face meeting.
Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia
Authors: Avetyan Diana , Hakobyan Siras , Nikoghosyan Maria , Khachatryan Gisane , Sirunyan Tamara , Muradyan Nelli , Zakharyan Roksana , Chavushyan Andranik , Ghazaryan Hovsep , Melkonyan Ani , Stepanyan Ani , Hayrapetyan Varduhi , Atshemyan Sofi , Martirosyan Gevorg , Melik-Andreasyan Gayane , Sargsyan Shushan , Ghazazyan Armine , Aleksanyan Naira , Nersisyan Lilit , Arakelyan Arsen 
Published: June 2021

AbstractSequencing of SARS-CoV-2 provides essential information into viral evolution, transmission, and epidemiology. Short-read next-generation sequencing platforms are currently the gold-standard approaches characterized by the highest accuracy. Meanwhile, Oxford Nanopore’s long-read sequencing devices show great promise, offering comparable accuracy, fast turnaround time, and reduced cost. In this study, we performed whole-genome sequencing and molecular-genetic characterization of SARS-CoV-2 from clinical specimens using an amplicon-based nanopore sequencing approach. Lineage and phylogenetic analysis identified the most prevalent lineages at different time points (B.1.1.163, B.1.1.208, B.1.1, and since March 2021 - B.1.1.7). In addition, we evaluated the possible effect of identified mutations on the efficacy of recommended primers and probes used for PCR detection of SARS-CoV-2. In summary, a high-quality SARS-CoV-2 genome can be acquired by nanopore sequencing and it can serve as an efficient and affordable alternative to short-read next-generation sequencing and be used for epidemiologic surveillance and molecular-genetic analyses of the virus.
White Blood Cell and Platelet Dynamics Define Human Inflammatory Recovery
Authors: Foy Brody H , Sundt Thor , Carlson Jonathan C T , Aguirre Aaron D , Higgins John M 
Published: June 2021

AbstractInflammation is the physiologic reaction to cellular and tissue damage caused by pathologic processes including trauma, infection, and ischemia1. Effective inflammatory responses integrate molecular and cellular functions to prevent further tissue damage, initiate repair, and restore homeostasis, while futile or dysfunctional responses allow escalating injury, delay recovery, and may hasten death2. Elevation of white blood cell count (WBC) and altered levels of other acute phase reactants are cardinal signs of inflammation, but the dynamics of these changes and their resolution are not established3,4. Patient responses appear to vary dramatically with no clearly defined signs of good prognosis, leaving physicians reliant on qualitative interpretations of laboratory trends4,5.We retrospectively, observationally studied the human acute inflammatory response to trauma, ischemia, and infection by tracking the longitudinal dynamics of cellular and serum markers in hospitalized patients. Unexpectedly, we identified a conserved pattern of recovery defined by co-regulation of WBC and platelet (PLT) populations. Across all inflammatory conditions studied, recovering patients followed a consistent WBC-PLT trajectory shape that is well-approximated by exponential WBC decay and delayed linear PLT growth. This recovery trajectory shape may represent a fundamental archetype of human physiologic response at the cellular population scale, and provides a generic approach for identifying high-risk patients: 32x relative risk of adverse outcomes for cardiac surgery patients, 9x relative risk of death for COVID-19, and 5x relative risk of death for myocardial infarction.
Reduction in severity of all-cause gastroenteritis requiring hospitalisation in children vaccinated against rotavirus in Malawi
Authors: Mandolo Jonathan J. , Henrion Marc Y. R. , Mhango Chimwemwe , Chinyama End , Wachepa Richard , Kanjerwa Oscar , Malamba-Banda Chikondi , Shawa Isaac T. , Hungerford Daniel , Kamng’ona Arox W. , Iturriza-Gomara Miren , Cunliffe Nigel A. , Jere Khuzwayo C. 
Published: June 2021

AbstractBackgroundRotavirus is the major cause of severe gastroenteritis in children aged <5 years. Introduction of Rotarix® rotavirus vaccine (RV1) in Malawi in 2012 has reduced rotavirus-associated hospitalisations and diarrhoeal mortality. However, RV1 impact on gastroenteritis severity remains unknown. We conducted a hospital-based surveillance study to assess RV1 impact on gastroenteritis severity in children aged <5 years, in Malawi.MethodsStool samples were collected from children hospitalised with acute gastroenteritis from December 2011 – October 2019. Gastroenteritis severity was determined using Ruuska and Vesikari scores. Rotavirus was detected in stool using Enzyme Immunoassay. Rotavirus genotypes were determined using nested RT-PCR. Associations between RV1 vaccination and gastroenteritis severity were investigated using adjusted linear regression.ResultsIn total, 3,159 children were recruited. After adjusting for Mid-Upper Arm Circumference, age, weight, gender and receipt of other vaccines, all-cause gastroenteritis severity scores were 2.21 units lower (95% CI 1.85, 2.56; p<0.001) among RV1-vaccinated (n=2,224) compared to RV1-unvaccinated children (n=935); the decrease was comparable between rotavirus-positive and rotavirus-negative cases in all age groups. The reduction in severity score was observed against every rotavirus genotype, although the magnitude was smaller among those infected with G12P[6] compared to the remaining genotypes (p=0.011). Other than RV1 vaccination, age was the only variable associated with gastroenteritis severity. Each one-year increment in age was associated with a decrease of 0.43 severity score (95% CI 0.26, 0.60; p<0.001).ConclusionOur findings provide additional evidence of RV1 impact in a high disease burden, low-income country, lending further support to Malawi’s rotavirus vaccine programme.SummaryIn a long-term hospital-based surveillance study in Malawi, we found evidence of the reduction in gastroenteritis severity among hospitalised RV1-vaccinated children infected with both homotypic and heterotypic rotavirus strains and off-target RV1 vaccine effects against non-rotavirus diarrhoeal severity.
Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag
Authors: Akdogan-Ozdilek Bagdeser , Duval Katherine L , Meng Fanju W , Murphy Patrick J , Goll Mary G 
Published: June 2021

AbstractBackgroundCell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis.ResultsTo overcome these challenges, we adapted the chromatin profiling methods CUT&RUN and CUT&Tag for use in zebrafish, and applied these methods to generate high resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z from mid gastrula stage embryos. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences.ConclusionsOur results demonstrate the power of combining CUT&RUN and CUT&Tag methods with the strengths of the zebrafish system to define emerging chromatin landscapes in the context of vertebrate embryogenesis.
The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure
Authors: González-Solares Eduardo A. , Dariush Ali , González-Fernández Carlos , Yoldaş Aybüke Küpcü , Sa’d Mohammad Al , Millar Neil , Whitmarsh Tristan , Chornay Nicholas , Falciatori Ilaria , Fatemi Atefeh , Goodwin Daniel , Kuett Laura , Mulvey Claire M. , Páez Ribes Marta , Qosaj Fatime , Roth Andrew , Vázquez-García Ignacio , Watson Spencer S. , Windhager Jonas , Aparicio Samuel , Bodenmiller Bernd , Boyden Ed , Caldas Carlos , Harris Owen , Shah Sohrab P. , Tavaré Simon ,   CRUK IMAXT Grand Challenge Team, Bressan Dario , Hannon Gregory J. , Walton Nicholas A. 
Published: June 2021

AbstractWith the aim of producing a 3D representation of tumours, IMAXT uses a large variety of modalities in order to acquire tumour samples and produce a map of every cell in the tumour and its host environment. With the large volume and variety of data produced in the project we develop automatic data workflows and analysis pipelines and introduce a research methodology where scientists connect to a cloud environment to perform analysis close to where data are located instead of bringing data to their local computers. Here we present the data and analysis infrastructure, discuss the unique computational challenges and describe the analysis chains developed and deployed to generate molecularly annotated tumour models. Registration is achieved by use of a novel technique involving spherical fiducial marks that are visible in all imaging modalities used within IMAXT.
Proteome-wide probing of the dual NMT-dependent myristoylation tradeoff unveils potent, mechanism-based suicide inhibitors
Authors: Rivière Frédéric , Dian Cyril , Dutheil Rémi F. , Giglione Carmela , Meinnel Thierry 
Published: June 2021

ABSTRACTN-myristoyltransferases (NMTs) catalyze protein myristoylation, a major and ubiquitous lipid modification. Originally thought to modify only N-terminal glycine α-amino groups (G-myristoylation), NMTs are now known to modify lysine ε-amino groups (K-myristoylation), the significance of which is uncertain. Here we exploited systematic structural proteomics analyses and a novel pipeline involving the Shigella IpaJ protease to discriminate K- and G-myristoylation with unprecedented accuracy and identify the specific features driving each modification. NMT-dependent K-myristoylation occurs post-translationally and only on lysines 1, 2, or 3 following G-myristoylation or caspase cleavage. Direct interactions between the substrate’s reactive amino group and the NMT catalytic base slow K-myristoylation catalysis. IpaJ unmasked novel K-myristoylation sites in a dozen human proteins. The unique properties of NMT-driven K-myristoylation allowed us to design potent, mechanism-based suicide NMT inhibitors. These analyses unravel the respective paths towards K-myristoylation, G-myristoylation, or NMT inhibition, which rely on a very subtle tradeoff embracing the chemical landscape around the reactive group.SIGNIFICANCE STATEMENTWe report the specific and unique elements guiding N-myristoyltransferase to either alpha or epsilon myristoylation, allowing us to establish the post-translational nature of N-myristoyltransferase-dependent lysine myristoylation and design novel, potent N-myristoyltransferase inhibitors.
Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage
Authors: Zhao Zhe , Fagerlund Riku , Sauter Daniel , Tossavainen Helena , Permi Perttu , Kirchhoff Frank , Saksela Kalle 
Published: June 2021

ABSTRACTThe accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy - termed the “R-clamp” - that favors the formation of this salt bridge via buttressing Arg77. Comparison of evolutionarily diverse Nef proteins revealed that several distinct R-clamps have evolved that are functionally equivalent but differ in the side chain compositions of Nef residues 83 and 120. Whereas a similar R-clamp design is shared by Nef proteins of HIV-1 groups M, O, and P, as well as SIVgor, the Nef proteins of SIV from the Eastern chimpanzee subspecies (SIVcpzP.t.s.) exclusively utilize another type of R-clamp. By contrast, SIV of Central chimpanzees (SIVcpzP.t.t.) and HIV-1 group N strains show more heterogenous R-clamp design principles, including a non-functional evolutionary intermediate of the aforementioned two classes. These data add to our understanding of the structural basis of SH3 binding and kinase deregulation by Nef, and provide an interesting example of primate lentiviral protein evolution.AUTHOR SUMMARYViral replication depends on interactions with a plethora of host cell proteins. Cellular protein interactions are typically mediated by specialized binding modules, such as the SH3 domain. To gain access to host cell regulation viruses have evolved to contain SH3 domain binding sites in their proteins, a notable example of which is the HIV-1 Nef protein. Here we show that during the primate lentivirus evolution the structural strategy that underlies the avid binding of Nef to cellular SH3 domains, which we have dubbed the R-clamp, has been generated via alternative but functionally interchangeable molecular designs. These patterns of SH3 recognition depend on the amino acid combinations at the positions corresponding to residues 83 and 120 in the consensus HIV-1 Nef sequence, and are distinctly different in Nef proteins from SIVs of Eastern and Central chimpanzees, gorillas, and the four groups of HIV-1 that have independently originated from the latter two. These results highlight the evolutionary plasticity of viral proteins, and have implications on therapeutic development aiming to interfere with SH3 binding of Nef.
SIA: Selection Inference Using the Ancestral Recombination Graph
Authors: Hejase Hussein A. , Mo Ziyi , Campagna Leonardo , Siepel Adam 
Published: June 2021

AbstractDetecting signals of selection from genomic data is a central problem in population genetics. Coupling the rich information in the ancestral recombination graph (ARG) with a powerful and scalable deep learning framework, we developed a novel method to detect and quantify positive selection: Selection Inference using the Ancestral recombination graph (SIA). Built on a Long Short-Term Memory (LSTM) architecture, a particular type of a Recurrent Neural Network (RNN), SIA can be trained to explicitly infer a full range of selection coefficients, as well as the allele frequency trajectory and time of selection onset. We benchmarked SIA extensively on simulations under a European human demographic model, and found that it performs as well or better as some of the best available methods, including state-of-the-art machine-learning and ARG-based methods. In addition, we used SIA to estimate selection coefficients at several loci associated with human phenotypes of interest. SIA detected novel signals of selection particular to the European (CEU) population at the MC1R and ABCC11 loci. In addition, it recapitulated signals of selection at the LCT locus and several pigmentation-related genes. Finally, we reanalyzed polymorphism data of a collection of recently radiated southern capuchino seedeater taxa in the genus Sporophila to quantify the strength of selection and improved the power of our previous methods to detect partial soft sweeps. Overall, SIA uses deep learning to leverage the ARG and thereby provides new insight into how selective sweeps shape genomic diversity.
Prevalence of white matter pathways coming into a single diffusion MRI voxel orientation: the bottleneck issue in tractography
Authors: Schilling Kurt G , Tax Chantal M.W. , Rheault Francois , Landman Bennett , Anderson Adam , Descoteaux Maxime , Petit Laurent 
Published: June 2021

AbstractCharacterizing and understanding the limitations of diffusion MRI fiber tractography is a prerequisite for methodological advances and innovations which will allow these techniques to accurately map the connections of the human brain. The so-called “crossing fiber problem” has received tremendous attention and has continuously triggered the community to develop novel approaches for disentangling distinctly oriented fiber populations. Perhaps an even greater challenge occurs when multiple white matter bundles converge within a single voxel, or throughout a single brain region, and share the same parallel orientation, before diverging and continuing towards their final cortical or sub-cortical terminations. These so-called “bottleneck” regions contribute to the ill-posed nature of the tractography process, and lead to both false positive and false negative estimated connections. Yet, as opposed to the extent of crossing fibers, a thorough characterization of bottleneck regions has not been performed. The aim of this study is to quantify the prevalence of bottleneck regions. To do this, we use diffusion tractography to segment known white matter bundles of the brain, and assign each bundle to voxels they pass through and to specific orientations within those voxels (i.e. fixels). We demonstrate that bottlenecks occur in greater than 50-70% of fixels in the white matter of the human brain. We find that all projection, association, and commissural fibers contribute to, and are affected by, this phenomenon, and show that even regions traditionally considered “single fiber voxels” often contain multiple fiber populations. Together, this study shows that a majority of white matter presents bottlenecks for tractography which may lead to incorrect or erroneous estimates of brain connectivity or quantitative tractography (i.e., tractometry), and underscores the need for a paradigm shift in the process of tractography and bundle segmentation for studying the fiber pathways of the human brain.
Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4
Authors: Neijenhuis Tim , van Keulen Siri C. , Bonvin Alexandre M.J.J. 
Published: June 2021

AbstractA wide range of cellular processes require the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The produced density maps can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low-to-medium resolution maps. Unfortunately, the produced models frequently contain atomic clashes at the protein-protein interfaces (PPIs) as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best performing protocol, consisting of a semi-flexible simulated annealing refinement with restraints on the centroids of the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.
PI(4,5)P2 controls slit diaphragm formation and endocytosis in Drosophila nephrocytes
Authors: Gass Maximilian , Borkowsky Sarah , Lotz Marie-Luise , Schröter Rita , Nedvetsky Pavel , Luschnig Stefan , Rohlmann Astrid , Missler Markus , Krahn Michael P. 
Published: June 2021

SUMMARYDrosophila nephrocytes are an emerging model system for mammalian podocytes and podocyte-associated diseases. Like podocytes, nephrocytes exhibit characteristics of epithelial cells, but the role of phospholipids in polarization of these cells is yet unclear. In epithelia phosphatidylinositol(4,5)bisphosphate (PI(4,5)P2) and phosphatidylinositol(3,4,5)-trisphosphate (PI(3,4,5)P3) are asymmetrically distributed in the plasma membrane and determine apical-basal polarity. Here we demonstrate that both phospholipids are present in the plasma membrane of nephrocytes, but only PI(4,5)P2 accumulates at slit diaphragms. Knockdown of Skittles, a phosphatidylinositol(4)phosphate 5-kinase, which produces PI(4,5)P2, abolished slit diaphragm formation and led to strongly reduced endocytosis. Notably, reduction in PI(3,4,5)P3 by overexpression of PTEN or expression of a dominant-negative phosphatidylinositol-3-Kinase did not affect nephrocyte function, whereas enhanced formation of PI(3,4,5)P3 by constitutively active phosphatidylinositol-3-Kinase resulted in strong slit diaphragm and endocytosis defects by ectopic activation of the Akt/mTOR pathway. Thus, PI(4,5)P2 but not PI(3,4,5)P3 is essential for slit diaphragm formation and nephrocyte function. However, PI(3,4,5)P3 has to be tightly controlled to ensure nephrocyte development.