bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substrate specificity profiling of SARS-CoV-2 main protease enables design of activity-based probes for patient-sample imaging
Authors: Rut Wioletta , Groborz Katarzyna , Zhang Linlin , Sun Xinyuanyuan , Zmudzinski Mikolaj , Pawlik Bartlomiej , Młynarski Wojciech , Hilgenfeld Rolf , Drag Marcin 
Published: March 2020

AbstractIn December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed in Wuhan, China. Due to international travel and human-to-human transmission, the virus spread rapidly inside and outside of China. Currently, there is no effective antiviral treatment for coronavirus disease 2019 (COVID-19); therefore, research efforts are focused on the rapid development of vaccines and antiviral drugs. The SARS-CoV-2 main protease constitutes one of the most attractive antiviral drug targets. To address this emerging problem, we have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases, using natural and a large panel of unnatural amino acids. On the basis of these findings, we designed and synthesized an inhibitor and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. Using this approach we visualized SARS-CoV-2 active Mprowithin nasopharyngeal epithelial cells of a patient with active COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents or diagnostic tests.
Transcranial ultrasound stimulation in humans is associated with an auditory confound that can be effectively masked
Authors: Braun Verena , Blackmore Joseph , Cleveland Robin O. , Butler Christopher R. 
Published: March 2020

AbstractBackgroundTranscranial ultrasound stimulation (TUS) is emerging as a potentially powerful, non-invasive technique for focal brain stimulation. Recent animal work suggests, however, that TUS effects may be confounded by indirect stimulation of early auditory pathways.ObjectiveWe aimed to investigate in human participants whether TUS elicits audible sounds and if these can be masked by an audio signal.MethodsIn 18 healthy participants, T1-weighted magnetic resonance brain imaging was acquired for 3D ultrasound simulations to determine optimal transducer placements and source amplitudes. Thermal simulations ensured that temperature rises were <0.5 °C at the target and <3 °C in the skull. To test for non-specific auditory activation, TUS (500 kHz, 300 ms burst, modulated at 1 kHz with 50% duty cycle) was applied to primary visual cortex and participants were asked to distinguish stimulation from non-stimulation trials. EEG was recorded throughout the task. Furthermore, ex-vivo skull experiments tested for the presence of skull vibrations during TUS.ResultsWe found that participants can hear sound during TUS and can distinguish between stimulation and non-stimulation trials. This was corroborated by EEG recordings indicating auditory activation associated with TUS. Delivering an audio waveform to participants through earphones while TUS was applied reduced detection rates to chance level and abolished the TUS-induced auditory EEG signal. Ex vivo skull experiments demonstrated that sound is conducted through the skull at the pulse repetition frequency of the ultrasound.ConclusionFuture studies using TUS in humans need to take this auditory confound into account and mask stimulation appropriately.
Single-cell transcriptomics of allo-reactive CD4+T cells over time reveals divergent fates during gut GVHD
Authors: Engel Jessica A. , Lee Hyun Jae , Williams Cameron G. , Kuns Rachel , Olver Stuart , Lansink Lianne I. M. , Soon Megan S. F. , Andersen Stacey B. , Powell Joseph E. , Svensson Valentine , Teichmann Sarah A. , Hill Geoffrey R , Varelias Antiopi , Koyama Motoko , Haque Ashraful 
Published: March 2020

AbstractAcute gastrointestinal Graft-versus-Host-Disease (GVHD) is a primary determinant of mortality after allogeneic hematopoietic stem-cell transplantation (alloSCT). It is mediated by alloreactive donor CD4+T cells that differentiate into pathogenic subsets expressing IFNγ, IL-17A or GM-CSF, and is regulated by subsets expressing IL-10 and/or Foxp3. Developmental relationships between T-helper states during priming in mesenteric lymph nodes (mLN) and effector function in the GI tract remain undefined at genome-scale. We used scRNA-seq and computational modelling to create an atlas of putative differentiation pathways during GVHD. Computational trajectory inference suggested emergence of pathogenic and regulatory states along a single developmental trajectory in mLN. Importantly, we identified an unexpected second trajectory, categorised by little proliferation or cytokine expression, reduced glycolysis, and high TCF1 expression. TCF1hicells upregulated α4β7 prior to gut migration and failed to express cytokines therein. Nevertheless, they demonstrated recall potential and plasticity following secondary transplantation, including cytokine or Foxp3 expression, but reduced TCF1. Thus, scRNA-seq revealed divergence of allo-reactive CD4+T cells into quiescent and effector states during gut GVHD, reflecting putative heterogenous primingin vivo. These findings, the first at a single-cell level during GVHD over time, can now be used to interrogate T cell differentiation in patients undergoing alloSCT.
Real-time Ratiometric Imaging of Micelles Assembly State in a Microfluidic Cancer-on-a-chip
Authors: Feiner-Gracia Natalia , Mares Adrianna Glinkowska , Buzhor Marina , Rodriguez-Trujillo Romen , Samitier Josep , Amir Roey J. , Pujals Silvia , Albertazzi Lorenzo 
Published: March 2020

ABSTRACTThe performance of supramolecular nanocarriers as drug delivery systems depends on their stability in the complex and dynamic biological media. After administration, nanocarriers are challenged by confronting different barriers such as shear stress and proteins present in blood, endothelial wall, extracellular matrix and eventually cancer cell membranes. While early disassembly will result in a premature drug release, extreme stability of the nanocarriers can lead to poor drug release and low efficiency. Therefore, comprehensive understanding of the stability and assembly state of supramolecular carriers in each stage of delivery is a key factor for the rational design of these systems. One of the key challenges is that current 2Din vitromodels do not provide exhaustive information, as they do not fully recapitulate the 3D tumor microenvironment. This deficiency of the 2D models complexity is the main reason for the differences observedin vivowhen testing the performance of supramolecular nanocarriers. Herein, we present a real-time monitoring study of self-assembled micelles stability and extravasation, combining spectral confocal microscopy and a microfluidic tumor-on-a-chip. The combination of advanced imaging and a reliable organ-on-a-chip model allow us to track micelle disassembly by following the spectral properties of the amphiphiles in space and time during the crucial steps of drug delivery. The spectrally active micelles were introduced under flow and their position and conformation followed during the crossing of barriers by spectral imaging, revealing the interplay between carrier structure, micellar stability and extravasation. Integrating the ability of the micelles to change their fluorescent properties when disassembled, spectral confocal imaging and 3D microfluidic tumor blood vessel-on-a-chip, resulted in the establishment of a robust testing platform, suitable for real-time imaging and evaluation of supramolecular drug delivery carrier’s stability.
Robust Production of Uniform Human Cerebral Organoids from Pluripotent Stem Cells
Authors: Sivitilli A. , Gosio J.T. , Ghoshal B. , Evstratova A. , Trcka D. , Ghiasiighorveh P. , Hernandez J. J. , Beaulieu J. M. , Wrana J. L. , Attisano L. 
Published: March 2020

AbstractHuman cerebral organoid (hCO) models offer the opportunity to understand fundamental processes underlying human specific cortical development and pathophysiology in an experimentally tractable system. While diverse methods to generate brain organoids have been developed, a major challenge has been the production of organoids with reproducible cell type heterogeneity and macroscopic morphology. Here, we directly addressed this problem by establishing a robust production pipeline to generate morphologically consistent (ie uniform) hCOs and achieve a success rate of >80%. These hCOs include both a radial glial stem cell compartment and electrophysiologically competent mature neurons. Moreover, we show using immunofluorescence microscopy and single cell profiling, that individual organoids display reproducible cell type compositions that are conserved upon extended culture. We expect that application of this method will provide new insights into brain development and disease processes.
Anatomically precise relationship between specific amygdala connections and selective markers of mental well-being in humans
Authors: Klein-Flügge Miriam C , Jensen Daria EA , Takagi Yu , Verhagen Lennart , Smith Stephen M , Rushworth Matthew FS 
Published: March 2020

AbstractThere has been increasing interest in using neuroimaging measures to predict psychiatric disorders. However, predictions usually rely on large numbers of brain connections and large disorder heterogeneity, thus lacking both anatomical and behavioural specificity, preventing the advancement of targeted interventions. Here, we address both challenges. First, using resting-state functional MRI, we parcellated the amygdala, a region implicated in mood disorders but difficult to image with high fidelity, into seven nuclei. Next, a questionnaire factor analysis provided four sub-clinical latent behaviours frequently found in anxious-depressive individuals, such as negative emotions and sleep problems. Finally, for each latent behaviour, we identified the most predictive connections between individual amygdala nuclei and highly specific regions of interest e.g. dorsal raphe nucleus in the brainstem or medial prefrontal cortical regions. A small number of distinct connections predicted behaviours, providing unprecedented levels of specificity, in humans, for relating mental well-being to precise anatomical connections.
Conjugates of neuroprotective chaperone L-PGDS provide MRI contrast for detection of amyloid β-rich regions in live Alzheimer’s Disease mouse model brain
Authors: Sharma Bhargy , Grandjean Joanes , Phillips Margaret , Kumar Ambrish , Mandino Francesca , Yeow Ling Yun , Nandwana Vikas , Dravid Vinayak P. , Bengang Xing , Lim Sierin , Pervushin Konstantin 
Published: March 2020

AbstractEndogenous brain proteins can recognize the toxic oligomers of amyloid-β (Aβ) peptides implicated in Alzheimer’s disease (AD) and interact with them to prevent their aggregation. Lipocalin-type Prostaglandin D Synthase (L-PGDS) is a major Aβ-chaperone protein in the human cerebrospinal fluid. Here we demonstrate that L-PGDS detects amyloids in diseased mouse brain. Conjugation of L-PGDS with magnetic nanoparticles enhanced the contrast for magnetic resonance imaging. We conjugated the L-PGDS protein with ferritin nanocages to detect amyloids in the AD mouse model brain. We show here that the conjugates administered through intraventricular injections co-localize with amyloids in the mouse brain. These conjugates can target the brain regions through non-invasive intranasal administration, as shown in healthy mice. These conjugates can inhibit the aggregation of amyloidsin vitroand show potential neuroprotective function by breaking down the mature amyloid fibrils.
Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides
Authors: Mlýnský Vojtěch , Kührová Petra , Kühr Tomáš , Otyepka Michal , Bussi Giovanni , Banáš Pavel , Šponer Jiří 
Published: March 2020

ABSTRACTDetermination of RNA structural-dynamic properties is challenging for experimental methods. Thus atomistic molecular dynamics (MD) simulations represent a helpful technique complementary to experiments. However, contemporary MD methods still suffer from limitations of force fields (ffs), including imbalances in the non-bondedffterms. We have recently demonstrated that some improvement of state-of-the-art AMBER RNAffcan be achieved by adding a new term for H-bonding called gHBfix, which increases tuning flexibility and reduces the risk of side-effects. Still, the first gHBfix version did not fully correct simulations of short RNA tetranucleotides (TNs). TNs are key benchmark systems due to availability of unique NMR data, although giving too much weight on improving TN simulations can easily lead to over-fitting to A-form RNA. Here we combine the gHBfix version with another term called tHBfix, which separately treats H-bond interactions formed by terminal nucleotides. This allows to refine simulations of RNA TNs without affecting simulations of other RNAs. The approach is in line with adopted strategy of current RNAffs, where the terminal nucleotides possess different parameters for the terminal atoms than the internal nucleotides. The combination of gHBfix with tHBfix significantly improves the behavior of RNA TNs during well-converged enhanced-sampling simulations. TNs mostly populate canonical A-form like states while spurious intercalated structures are largely suppressed. Still, simulations of r(AAAA) and r(UUUU) TNs show some residual discrepancies with the primary NMR data which suggests that future tuning of some otherffterms might be useful.
Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos
Authors: Zizka Vera Marie Alida , Weiss Martina , Leese Florian 
Published: March 2020

AbstractGenetic diversity is the most basal level of biodiversity and determines the evolutionary capacity of species to adapt to changing environments, yet it is typically neglected in routine biomonitoring and stressor impact assessment. For a comprehensive analysis of stressor impacts on genetic diversity, it is necessary to assess genetic variants simultaneously in many individuals and species. Such an assessment is not as straight-forward and usually limited to one or few individual species. However, nowadays species diversity can be assessed by analysing thousands of individuals of a community simultaneously with DNA metabarcoding. Recent bioinformatic advances also allow for the extraction of exact sequence variants (ESVs or haplotypes) in addition to Operational Taxonomic Units (OTUs). By using this new capability, we here evaluated if the analysis of mitochondrial genetic diversity in addition to species diversity can provide insights into responses of stream macrozoobenthic communities to environmental stressors. For this purpose, we analysed macroinvertebrate bulk samples of three German river systems with different stressor levels using DNA metabarcoding. While OTU and haplotype number were negatively correlated with stressor impact, this association was not as clear when looking at haplotype diversity. Here, stressor responses were only found for sensitive EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa, and those exceedingly resistant to organic stress. An increase in haplotype number per OTU and haplotype diversity of sensitive taxa was observed with an increase in ecosystem quality and stability, while the opposite pattern was detected for pollution resistant taxa. However, this pattern was less prominent than expected based on the strong differences in stressor intensity between sites. To compare genetic diversity among river systems, only OTUs could be used, which were present in all systems. As OTU composition differed strongly between the rivers, this led to the exclusion of a high number of OTUs, especially in diverse river systems of good quality, which potentially diminished the genetic diversity patterns. To better understand responses of genetic diversity to environmental stressors for example in river ecosystems, it would be important to increase OTU overlap between sites of comparisons, e.g. by sampling a narrower stressor gradient, and to perform calibrated studies controlling for the number and individual genotypes. However, this pioneer study shows that the extraction of haplotypes from DNA metabarcoding datasets is a promising tool to simultaneously assess mitochondrial genetic diversity changes in response to environmental impacts for a metacommunity.
Nutrient-dependent trade-offs between ribosomes and division protein synthesis control bacterial cell size and growth
Authors: Serbanescu Diana , Ojkic Nikola , Banerjee Shiladitya 
Published: March 2020

SUMMARYCell size control emerges from a regulated balance between the rates of cell growth and division. In bacteria, simple quantitative laws connect cellular growth rate to ribosome abundance. However, it remains poorly understood how translation regulates bacterial cell size and shapes under growth perturbations. Here we develop a whole-cell model for growth dynamics in rod-shaped bacteria that links ribosomal abundance with cell geometry, division control, and the extracellular environment. Our study reveals that cell size maintenance under nutrient perturbations requires a balanced trade-off between ribosomes and division protein synthesis. Deviations from this trade-off relationship are predicted under translational perturbations, leading to distinct modes of cell morphological changes, in agreement with single-cell experimental data onEscherichia coli. Furthermore, by calibrating our model with experimental data, we predict how combinations of nutrient-, translational- and shape perturbations can be chosen to optimize bacterial growth fitness and antibiotic resistance.
Exploring the outcomes of the external revealing of knowledge
Authors: Baima Gabriele , Santoro Gabriele , Busso Donatella , Quaglia Roberto 
Published: March 2020

PurposeThis paper explores the outcomes of the external revealing of knowledge. More specifically, we aim to understand how external revealing of knowledge can be seen as value creation in the craft beer industry.Design/methodology/approachA single-case study methodology is used to answer the research question “What are the outcomes of the external revealing of knowledge?”FindingsThe research highlights several dynamics and outcomes regarding the external revealing of knowledge, mainly connected to creating value for the industry, strengthening a firm's network, enhancing the culture of the territory, gaining access to knowledge, and guaranteeing market competitiveness.Originality/valueA few studies have addressed a specific aspect of outbound open innovation, which involves free revealing of knowledge to external stakeholders. Previous works are mostly conceptual; thus, there is a lack of empirical studies about revealing strategies. This research empirically analyzes the outcomes of the external revealing of knowledge and, more generally, of an open innovation approach.
The synergistic combination of fuzzy C-means and ensemble filtering for class noise detection
Authors: Nematzadeh Zahra , Ibrahim Roliana , Selamat Ali , Nazerian Vahdat 
Published: March 2020

Purpose
The purpose of this study is to enhance data quality and overall accuracy and improve certainty by reducing the negative impacts of the FCM algorithm while clustering real-world data and also decreasing the inherent noise in data sets.

Design/methodology/approach
The present study proposed a new effective model based on fuzzy C-means (FCM), ensemble filtering (ENS) and machine learning algorithms, called an FCM-ENS model. This model is mainly composed of three parts: noise detection, noise filtering and noise classification.

Findings
The performance of the proposed model was tested by conducting experiments on six data sets from the UCI repository. As shown by the obtained results, the proposed noise detection model very effectively detected the class noise and enhanced performance in case the identified class noisy instances were removed.

Originality/value
To the best of the authors’ knowledge, no effort has been made to improve the FCM algorithm in relation to class noise detection issues. Thus, the novelty of existing research is combining the FCM algorithm as a noise detection technique with ENS to reduce the negative effect of inherent noise and increase data quality and accuracy.
Line management attributions for effective HRM implementation
Authors: Bos-Nehles Anna , Van der Heijden Beatrice , Van Riemsdijk Maarten , Looise Jan Kees 
Published: March 2020

PurposeMany HRM practices are never thoroughly implemented, or are implemented ineffectively. To better understand what line managers need to implement HRM practices effectively, the authors have developed and validated a psychometrically sound measurement instrument dealing with line managers' attributions for effective HRM implementation. Based on the theory of causal attributions, the authors distinguish between internal and external attributions that determine how line managers implement HRM practices on the work floor.Design/methodology/approachA multidimensional approach has been used, and, after collecting data from 471 line managers, thorough scale development guidelines and validation procedures have been applied for instrument development.FindingsThe instrument's psychometric qualities have been assessed by calculating the reliability and validity of line managers' internal attributions – including its composing dimensions of desire and competences – and their external attributions – including the dimensions of support, capacity and policy and procedures. In particular, both convergent and discriminant validity as well as intra-class correlations have been established. The newly developed measures are found to be of good quality. The scales appear to discriminate well between the distinguished groups and show a good variation within groups.Practical implicationsThe developed measurement instrument helps HRM professionals to better understand line managers' attributions to effectively implement HRM practices and to provide them with support and training for effective HRM implementation.Originality/valuePrevious research has already identified weaknesses in HRM implementation, but lacked addressing the causes of this. The study presents antecedents for HRM implementation effectiveness, based on the causal attribution theory, and a psychometrically validated instrument to measure these antecedents.
HRM systems and employee affective commitment: the role of employee gender
Authors: Shin DuckJung , Garmendia Alaine , Ali Muhammad , Konrad Alison M. , Madinabeitia-Olabarria Damian 
Published: March 2020

PurposeDespite decades of studies on high-involvement human resource management (HRM) systems, questions remain of whether high-involvement HRM systems can increase the commitment of women. This study aims to contribute to the growing body of research on the cross-level effect of HRM systems and practices on employee affective commitment by considering the moderating role of gender.Design/methodology/approachIntegrating social exchange theory with gender role theory, this paper proposes that gender responses to HRM practices can be different. The hypotheses were tested using data from 104 small- and medium-sized retail enterprises and 6,320 employees from Spain.FindingsThe findings generally support the study’s hypotheses, with women’s affective commitment responding more strongly and positively to employees’ aggregated perceptions of a shop-level high-involvement HRM system. The findings imply that a high-involvement HRM system can promote the affective commitment of women.Originality/valueThis study investigates the impact of both an overall HRM system and function-specific HRM sub-systems (e.g. training, information, participation and autonomy). By showing that women can be more positively affected by high-involvement HRM systems, this paper suggests that high-involvement HRM systems can be used to encourage the involvement and participation of women.