bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers
Authors: Rosenke Kyle , Leventhal Shanna , Moulton Hong M. , Hatlevig Susan , Hawman David , Feldmann Heinz , Stein David A. 
Published: October 2020

SynopsisBackgroundSARS-CoV-2 is the causative agent of COVID-19 and a pathogen of immense global public health importance. Development of innovative direct-acting antiviral agents is sorely needed to address this virus. Peptide-conjugated morpholino oligomers (PPMO) are antisense agents composed of a phosphordiamidate morpholino oligomer covalently conjugated to a cell-penetrating peptide. PPMO require no delivery assistance to enter cells and are able to reduce expression of targeted RNA through sequence-specific steric blocking.Objectives and MethodsFive PPMO designed against sequences of genomic RNA in the SARS-CoV-2 5’-untranslated region and a negative control PPMO of random sequence were synthesized. Each PPMO was evaluated for its effect on the viability of uninfected cells and its inhibitory effect on the replication of SARS-CoV-2 in Vero-E6 cell cultures. Cell viability was evaluated with an ATP-based method and viral growth was measured with quantitative RT-PCR and TCID50infectivity assays.ResultsPPMO designed to base-pair with sequence in the 5’-terminal region or the leader transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, in a non-toxic and dose-responsive manner.ConclusionThe data indicate that PPMO have the ability to potently and specifically suppress SARS-CoV-2 growth and are promising candidates for further pre-clinical development.
A Genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms
Authors: Zhou Lili , Miller Caitlyn , Miraglia Loren J. , Romero Angelica , Mure Ludovic S. , Panda Satchidananda , Kay Steve A. 
Published: October 2020

AbstractThe regulatory mechanisms of circadian rhythms have been studied primarily at the level of the transcription-translation feedback loops of protein coding genes. Regulatory modules involving non-coding RNAs are less thoroughly understood. In particular, emerging evidence has revealed the important role of miRNAs in maintaining the robustness of the circadian system. To identify miRNAs that have the potential to modulate circadian rhythms, we conducted a genome-wide miRNA screen using U2OS luciferase reporter cells. Among 989 miRNAs in the library, 120 changed the period length in a dosage-dependent manner. We further validated the circadian regulatory function of a miRNA cluster, miR-183/96/182, bothin vitroandin vivo. We found that all three members of this miRNA cluster can modulate circadian rhythms. Particularly, miR-96 directly targeted a core circadian clock gene, PER2. The knockout of the miR-183/96/182 cluster in mice showed tissue-specific effects on circadian parameters and altered circadian rhythms at the behavioral level. This study identified a large number of miRNAs, including the miR-183/96/182 cluster, as circadian modulators. We provide a resource for further understanding the role of miRNAs in the circadian network and highlight the importance of miRNAs as a novel genome-wide layer of circadian clock regulation.Significance StatementAlthough miRNAs are emerging as important regulators of diverse physiological and pathological processes, our knowledge of their potential role in regulation of circadian rhythms is still limited. We deployed a cell-based genome-wide screening approach, and successfully identified mature miRNAs as cell-autonomous circadian modulators. We then specifically focused on the miR-183/96/182 cluster among the candidate miRNA hits and revealed their circadian function bothin vitroand invivofrom the unbiased screen. This study provides resources for further understanding the role of miRNAs in the circadian network. It also highlights the importance of miRNAs as a novel genome-wide layer of circadian clock regulation.
Effects of N-linked glycan of Lassa Virus Envelope Glycoprotein on the Immune Response
Authors: Zhu Xueqin , Liu Yang , Guo Jiao , Wang Zonglin , Cao Junyuan , Xiao Gengfu , Wang Wei 
Published: October 2020

AbstractLassa virus (LASV) belongs to theMammarenavirusgenus (family Arenaviridae) and causes severe hemorrhagic fever in humans. The glycoprotein precursor (GPC) contains eleven N-linked glycans that play essential roles in GPC functionalities such as cleavage, transport, receptor recognition, epitope shielding, and immune response. We used three mutagenesis strategies to abolish the individual glycan chains on the GPC and found that all three mutations led to cleavage inefficiency on the 2nd, 5th, and 8thglycosylation motifs. To evaluate N to Q mutagenesis for further research, it was found that deletion of the 2ndand 8thglycans completely inhibited the infectivity. We further investigated the role of glycans on GPC-mediated immune response by DNA immunization of mice. Deletion of the individual 1st, 3rd, 5thand 6thglycans significantly enhanced the proportion of effector CD4+ cells, whereas deletion of the 1st, 2nd, 3rd, 4th5th, 6th, and 9thglycans enhanced the proportion of CD8+ effector T cells. Deletion of specific glycans improves the Th1-type immune response, and abolishment of glycan on GPC generally increases the antibody titer to the glycan-deficient GPC. However, the antibodies from either the mutant or WT GPC-immunized mice show little neutralization effect on wild-type LASV. The glycan residues on GPC provide an immune shield for the virus, and thus represent a target for the design and development of a vaccine.ImportanceAt present, there are no Food and Drug Administration-approved drugs or vaccines specific for LASV. Similar to other enveloped viruses with a heavy glycan shield, the N-linked glycans of LASV make it difficult for effector T cells and neutralization antibodies to access the glycoprotein epitope. In this study, we evaluated the effect of the individual glycan chains on GPC-mediated immune response, and found that deletion of the glycan improves the proportion of effector T cells, improving the Th1-type immune response, and increasing the antibody titer to the WT and mutant GPC, which may be beneficial to vaccine design and development.
Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test
Authors: Bal Antonin , Pozzetto Bruno , Trabaud Mary-Anne , Escuret Vanessa , Rabilloud Muriel , Langlois-Jacques Carole , Paul Adèle , Guibert Nicolas , D’Aubarede Constance , Massardier-Pilonchery Amélie , Boibieux André , Morfin Florence , Pitiot Virginie , Gueyffier François , Lina Bruno , Fassier Jean-Baptiste , Trouillet-Assant Sophie ,   COVID SER STUDY GROUP
Published: October 2020

ObjectivesWe evaluated widely-used SARS-CoV-2 serological tests and their potential association with virus neutralization test (VNT) in a cohort of mild COVID-19 patients.MethodsA total of 439 specimens were longitudinally collected from 76 healthcare workers with RT-PCR-confirmed mild COVID-19. Nine serological assays developed by leading global companies (Abbott, DiaSorin, Siemens, Bio-Rad, Wantai, bioMérieux, Euroimmun) were assessed. For each test the sensitivity to detect SARS-CoV-2 antibodies was determined weekly after symptom onset. Correlation and concordance were assessed using the Spearman and Cohen’s Kappa coefficients, respectively. Positive percent agreement and negative percent agreement (NPA) with the VNT were also determined.ResultsThe Wantai Total Ab assay targeting the receptor binding domain (RBD) within the S protein presented the best sensitivity at different times during the course of disease. The best correlation between antibody level and neutralizing antibody titer was found with the Euroimmun S1-based IgA assay (Spearman coefficient [95%CI]: 0.71 [0.61-0.79]). A moderate concordance (Kappa [95%CI]: 0.43[0.23-0.63]) as well as the lowest NPA (33%) was found between the Wantai Total Ab assay and the VNT. Compared to the Wantai Total Ab assay, other total Ab or IgG assays targeting the S or the RBD (bioMérieux, DiaSorin, Siemens,) were more concordant with the VNT (Kappa>0.7 for the three tests) and had a higher NPA (range: 90% to 97%).ConclusionsAlthough some assays presented a better concordance with VNT than others, the present findings emphasize that commercialized serological tests including those targeting the RBD cannot substitute VNT for the assessment of functional antibody response.
An integrated clinical and genetic model for predicting risk of severe COVID-19
Authors: Dite Gillian S. , Murphy Nicholas M. , Allman Richard 
Published: October 2020

AbstractBackgroundAge and gender are often the only considerations in determining risk of severe COVID-19. There is an urgent need for accurate prediction of the risk of severe COVID-19 for use in workplaces and healthcare settings, and for individual risk management.MethodsClinical risk factors and a panel of 64 single-nucleotide polymorphisms were identified from published data. We used logistic regression to develop a model for severe COVID-19 in 1,582 UK Biobank participants aged 50 years and over who tested positive for the SARS-CoV-2 virus: 1,018 with severe disease and 564 without severe disease. Model discrimination was assessed using the area under the receiver operating characteristic curve (AUC).ResultsA model incorporating the SNP score and clinical risk factors (AUC=0.786) had 111% better discrimination of disease severity than a model with just age and gender (AUC=0.635). The effects of age and gender are attenuated by the other risk factors, suggesting that it is those risk factors – not age and gender – that confer risk of severe disease. In the whole UK Biobank, most are at low or only slightly elevated risk, but one- third are at two-fold or more increased risk.ConclusionsWe have developed a model that enables accurate prediction of severe COVID-19. Continuing to rely on age and gender alone to determine risk of severe COVID-19 will unnecessarily classify healthy older people as being at high risk and will fail to accurately quantify the increased risk for younger people with comorbidities.
White matter neuroanatomical predictors of aphasic verb retrieval
Authors: Dresang Haley C. , Hula William D. , Yeh Fang-Cheng , Warren Tessa , Dickey Michael Walsh 
Published: October 2020

AbstractBackgroundCurrent neurocognitive models of language function have been primarily built from evidence regarding object naming, and their hypothesized white matter circuit mechanisms tend to be coarse-grained.MethodsIn this cross-sectional, observational study, we used novel correlational tractography to assess the white matter circuit mechanism behindverb retrieval, measured via action picture-naming performance in adults with chronic aphasia.ResultsThe analysis identified tracts implicated in current neurocognitive dual-stream models of language function, including the left inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, and arcuate fasciculus. However, the majority of tracts associated with verb retrieval were not ones included in dual-stream models of language function. Instead, they were projection pathways that connect frontal and parietal cortices to subcortical regions associated with motor functions, including the left corticothalamic pathway, frontopontine tract, parietopontine tract, corticostriatal pathway, and corticospinal tract.ConclusionsThese results highlight that cortico-subcortical projection pathways implicated in motor functions may be importantly related to language function. This finding is consistent with grounded accounts of cognition and may furthermore inform neurocognitive models.Impact StatementThis study suggests that in addition to traditional dual-stream language fiber tracts, the integrity of projection pathways that connect frontal and parietal cortices to subcortical motor regions may be critically associated with verb-retrieval impairments in adults with aphasia. This finding challenges neurological models of language function.
Differential effects of emotional valence on mnemonic performance with greater hippocampal maturity
Authors: Kimbler Adam , McMakin Dana , Tustison Nicholas J. , Mattfeld Aaron T. 
Published: October 2020

AbstractThe hippocampal formation (HF) facilitates the creation of declarative memories, with subfields providing unique contributions to the discriminability and generalizability of events. The HF itself and its connections with other structures exhibit a protracted development. Maturational differences across subfields facilitate a shift towards memory specificity, with peri-puberty sitting at the inflection point. Peri-puberty also happens to be a sensitive period in the development of anxiety disorders. Taken together, we believe HF development is critical to negative overgeneralization, a common feature of anxiety disorders. To investigate the role of the HF in behavioral discrimination and generalization we examined the relation between behavior and cross-sectional indices of HF maturity derived from subfield volume. Participants aged 9-14 years, recruited from clinical and community sources, performed a recognition task with emotionally valent (positive, negative) and neutral images. T1-weighted and diffusion-weighted structural scans were collected. Partial least squares correlations were used to derive a singular metric of maturity for both HF volume and structural connectivity. We found our volumetric HF maturity index was positively associated with discrimination for neutral images and generalization for negative images. Hippocampal-medial prefrontal cortex structural connectivity maturity metric evidenced a similar trend with behavior as the HF volumetric approach. These findings are important because they reflect a novel developmentally related balance between discrimination and generalization behavior supported by the hippocampus and its connections with other regions. Maturational shifts in this balance may contribute to negative overgeneralization, a common feature of anxiety disorders that escalates during the same developmental window.Significance StatementThe hippocampal formation (HF) facilitates declarative memory specificity and is composed of subfields whose development during adolescence overlaps with the onset of anxiety disorders. Aberrations in mechanisms governing memory specificity may contribute to negative overgeneralization in anxious youth. Participants completed an emotional memory discrimination task while in the scanner. Using a multivariate maturity metric based on subfield volume we found individuals with more “mature” HF were better at differentiating similar neutral images and more likely to generalize similar negative images. These findings are important because they capture a novel developmental mechanism related to the balance between discrimination and generalization. Shifts in this balance, may contribute to negative overgeneralization, a common feature of anxiety disorders.
Assessment of Software Methods for Estimating Protein-Protein Relative Binding Affinities
Authors: Gonzalez Tawny R. , Martin Kyle P. , Barnes Jonathan E. , Patel Jagdish Suresh , Ytreberg F. Marty 
Published: October 2020

AbstractA growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < −0.5 kcal/mol) with high (83-98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.
Similar sensorimotor transformations control balance during standing and walking
Authors: Afschrift Maarten , De Groote Friedl , Jonkers Ilse 
Published: October 2020

AbstractStanding and walking balance control in humans relies on the transformation of sensory information to motor commands that drive muscles. Here, we evaluated whether sensorimotor transformations underlying walking balance control can be described by task-level center of mass kinematics feedback similar to standing balance control. We found that delayed feedback of center of mass position and velocity, but not local feedback of joint positions and velocities, can explain reactive ankle muscle activity and joint moments in response to perturbations of walking across protocols (discrete and continuous platform translations and discrete pelvis pushes). Feedback gains were modulated during the gait cycle and decreased with walking speed. Our results thus suggest that similar task-level variables, i.e. center of mass position and velocity, are controlled across standing and walking but that feedback gains are modulated during gait to accommodate changes in body configuration during the gait cycle and in stability with walking speed. These findings have important implications for modelling the neuromechanics of human balance control and for biomimetic control of wearable robotic devices. The feedback mechanisms we identified can be used to extend the current neuromechanical models that lack balance control mechanisms for the ankle joint. When using these models in the control of wearable robotic devices, we believe that this will facilitate shared control of balance between the user and the robotic device.
The impact of water deficit and heat stress combination on the molecular response, physiology and seed production of soybean
Authors: Cohen Itay , Zandalinas Sara I. , Fritschi Felix B. , Sengupta Soham , Fichman Yosef , Azad Rajeev K. , Mittler Ron 
Published: October 2020

AbstractA combination of drought and heat stress, occurring at the vegetative or reproductive growth phase of many different crops, can have a devastating impact on yield. In soybean (Glycine max), a considerable effort has been made to develop genotypes with enhanced yield production under conditions of drought or heat stress. However, how these genotypes perform in terms of growth, physiological responses and most importantly seed production, under conditions of drought and heat combination is mostly unknown. Here, we studied the impact of water deficit and heat stress combination on the physiology, seed production and yield per plant of two soybean genotypes, Magellan and Plant Introduction (PI) 548313, that differ in their reproductive responses to heat stress. Our findings reveal that although PI 548313 produced more seeds than Magellan under conditions of heat stress, under conditions of water deficit and heat stress combination its seed production decreased. Because number of flowers and pollen germination of PI 548313 remained high under heat or water deficit and heat combination, the reduced seed production exhibited by PI 548313 under the stress combination could be a result of processes that occur at the stigma, ovaries and/or other parts of the flower following pollen germination.HighlightTolerance to heat stress was found not to confer tolerance to a combination of water deficit and heat stress in soybean, highlighting the need for breeding strategies targeting the stress combination.
Hallmarks ofAlpha- andBetacoronavirusnon-structural protein 7+8 complexes
Authors: Krichel Boris , Bylapudi Ganesh , Schmidt Christina , Blanchet Clement , Schubert Robin , Brings Lea , Koehler Martin , Zenobi Renato , Svergun Dmitri , Lorenzen Kristina , Madhugiri Ramakanth , Ziebuhr John , Uetrecht Charlotte 
Published: October 2020

AbstractCoronaviruses infect many different species including humans. The last two decades have seen three zoonotic coronaviruses with SARS-CoV-2 causing a pandemic in 2020. Coronaviral non-structural proteins (nsp) built up the replication-transcription complex (RTC). Nsp7 and nsp8 interact with and regulate the RNA-dependent RNA-polymerase and other enzymes in the RTC. However, the structural plasticity of nsp7+8 complex has been under debate. Here, we present the framework of nsp7+8 complex stoichiometry and topology based on a native mass spectrometry and complementary biophysical techniques of nsp7+8 complexes from seven coronaviruses in the generaAlpha- andBetacoronavirusincluding SARS-CoV-2. Their complexes cluster into three groups, which systematically form either heterotrimers or heterotetramers or both, exhibiting distinct topologies. Moreover, even at high protein concentrations mainly heterotetramers are observed for SARS-CoV-2 nsp7+8. From these results, the different assembly paths can be pinpointed to specific residues and an assembly model is proposed.