bluuebunny/crossref_metadata_2025 huggingface dataset:
Personalizing deep brain stimulation using advanced imaging sequences
Authors: Neudorfer Clemens , Kroneberg Daniel , Al-Fatly Bassam , Goede Lukas , Kübler Dorothee , Faust Katharina , van Rienen Ursula , Tietze Anna , Picht Thomas , Herrington Todd M. , Middlebrooks Erik H. , Kühn Andrea , Schneider Gerd-Helge , Horn Andreas
Published: October 2021

Objective

With a growing appreciation for interindividual anatomical variability and patient-specific brain connectivity, advanced imaging sequences offer the opportunity to directly visualize anatomical targets for deep brain stimulation (DBS). The lack of quantitative evidence demonstrating their clinical utility, however, has hindered their broad implementation in clinical practice.

Methods

Using fast gray matter acquisition T1 inversion recovery (FGATIR) sequences, the present study identified a thalamic hypointensity that holds promise as a visual marker in DBS. To validate the clinical utility of the identified hypointensity we retrospectively analyzed 65 patients (26 female, mean age: 69.1±12.7 years) who underwent DBS in the treatment of essential tremor. We characterized its neuroanatomical substrates and evaluated the hypointensity’s ability to predict clinical outcome using stimulation volume modeling and voxel-wise mapping. Finally, we determined whether the hypointensity marker could predict symptom improvement on a patient-specific level.

Results

Anatomical characterization suggested that the identified hypointensity constituted the terminal part of the dentato-rubro-thalamic tract. Overlap between DBS stimulation volumes and the hypointensity in common space significantly correlated with tremor improvement (R2=0.16, p=0.017) and distance to hotspots previously reported in the literature (R2=0.49, p=7.9e-4). In contrast, the amount of variance explained by other anatomical atlas structures was reduced. When accounting for interindividual neuroanatomical variability, the predictive power of the hypointensity increased further (R2=0.37, p=0.002).

Interpretation

Our findings introduce and validate a novel imaging-based marker attainable from FGATIR sequences that has the potential to personalize and inform targeting and programming in DBS for essential tremor.
Transmission of SARS-CoV-2 in Norwegian schools: A population-wide register-based cohort study on characteristics of the index case and secondary attack rates
Authors: Rotevatn Torill Alise , Larsen Vilde Bergstad , Bjordal Johansen Tone Kristin , Astrup Elisabeth , Surén Pål , Greve-Isdahl Margrethe , Telle Kjetil
Published: October 2021

Objectives

To assess transmission of SARS-CoV-2 in schools mainly kept open during the COVID-19 pandemic.

Design

Population-wide register-based cohort study.

Setting

Primary and lower secondary schools in Norway have been open during the academic year 2020/2021 with strict infection prevention and control (IPC) measures in place. All identified contacts including student and staff members were urged to get tested following a positive SARS-CoV-2 case in a school.

Participants

All students and educational staff in Norwegian primary and lower secondary schools from August 2020 to June 2021.

Main outcome measures

Overall secondary attack rate (SAR14) was operationalized as the number of secondary cases (among students and/or staff) in the school by 14 days after the index case, divided by the number of students and staff members in the school. Moreover, we calculated SAR14-to-students, denoting transmission from all index cases to students only, SAR14-to-school staff, denoting transmission from all index cases to staff members only. We also calculated these measures in stratified samples consisting of student index cases or school staff index cases.

Results

From August 2020 to June 2021 there were 4,078 index cases, 79% were students and 21% were school staff. In the majority (55%) of schools with an index case, no secondary cases were observed by 14 days, and in 16% of the schools there were only one secondary case within 14 days. Overall SAR14 was found to be 0.33% (95%CI 0.32-0.33). Staff-to-staff transmission (SAR14 0.45%, 95%CI 0.40-0.52) was found to be slightly more common than student-to-student (SAR14 0.33%, 95%CI 0.32-0.34) and student-to-staff (SAR14 0.28%, 95%CI 0.25-0.30) transmission.

Conclusions

Our results confirm that schools have not been an important arena of transmission of SARS-CoV-2 in Norway and therefore support that schools can be kept open with IPC measures in place.
Personalized Computational Heart Models with T1-Mapped Fibrotic Remodeling Predict Risk of Sudden Death Risk in Patients with Hypertrophic Cardiomyopathy
Authors: O’Hara Ryan P. , Binka Edem , Prakosa Adityo , Zimmerman Stefan L. , Cartoski Mark J. , Abraham M. Roselle , Lu Dai-Yin , Boyle Patrick M. , Trayanova Natalia A.
Published: October 2021

Hypertrophic cardiomyopathy (HCM) causes sudden cardiac death (SCD) due to ventricular arrhythmias (VA) manifesting from myocardial fibrosis proliferation. Current clinical risk stratification criteria inadequately identify at-risk patients in need of primary prevention of VA. Here, we use mechanistic computational modeling of the heart to analyze how HCM-specific remodeling of the heart promotes arrhythmogenesis and to develop a personalized strategy to forecast risk of VAs in these patients. We combine contrast-enhanced cardiac magnetic-resonance (CMR) imaging and T1 mapping data to construct digital replicas of HCM patient hearts that represent the patient-specific distribution of focal and diffuse fibrosis and evaluate the substrate propensity to VA. Our analysis indicates that the presence of diffuse fibrosis, which is rarely assessed in these patients, increases arrhythmogenic propensity. In forecasting future VA events in HCM patients, the imaging-based computational heart approach achieved 84.6%, 76.9%, and 80.1% sensitivity, specificity, and accuracy, respectively, and significantly outperformed current clinical risk predictors. This novel VA risk assessment may have the potential to prevent SCD and help deploy primary prevention appropriately in HCM patients.
Spatial patterns of dental disease in patients with low salivary flow
Authors: Proctor Diana M. , Seiler Christof , Burns Adam R. , Walker Samuel , Jung Tina , Weng Jonathan , Sastiel Shanne , Rajendran Yoga , Kapila Yvonne , Millman Meredith E. , Armitage Gary C. , Loomer Peter M. , Holmes Susan P. , Ryder Mark I. , Relman David A.
Published: October 2021

Low salivary flow, or hyposalivation, is associated with an increased incidence of dental caries and a shift in their location from biting surfaces towards coronal and root surfaces. However, the relationship between salivary flow and periodontal disease is less clear. To identify clinical indicators of low salivary flow -- including the spatial pattern of dental and periodontal disease, features of the supra- and subgingival microbiota, and symptoms of dry mouth -- we enrolled individuals into two cohorts. The low flow cohort (N = 32) consisted of individuals with a presumptive diagnosis of the autoimmune disorder Sjögren’s Syndrome (SS) while the control cohort (N = 119) consisted of healthy controls. We constructed a series of tooth-specific linear models to quantify the extent to which patient cohort, age, and unstimulated whole salivary flow rate (UWS-FR), independent of each other, are associated with dental and periodontal disease at each tooth. While age and a diagnosis of SS correlated with the site-specific increment of disease so too did UWS-FR. Not only were lower UWS-FRs associated with a greater number of decayed, missing, or filled surfaces at 21 teeth, but they were also associated with increased recession, as measured by clinical attachment loss (CAL), at 10 teeth (adjusted p < 0.05). In addition, we examined microbiota community structure at different tooth sites using data from 427 subgingival and supragingival samples of 6 individuals and found that microbial dispersal is reduced in patients with low salivary flow, but only at supragingival and not at subgingival sites. Finally, we found that complaints by subjects of a negative impact on overall quality of life were associated with a UWS-FR less than 0.1 mL/min. Overall, our results suggest that novel predictors of hyposalivation can be identified by integrating clinical, microbial, and patient history data.
Poor neutralization and rapid decay of antibodies to SARS-CoV-2 variants in vaccinated dialysis patients
Authors: Bassi Jessica , Giannini Olivier , Silacci-Fregni Chiara , Pertusini Laura , Hitz Paolo , Terrot Tatiana , Franzosi Yves , Muoio Francesco , Saliba Christian , Meury Marcel , Dellota Exequiel A. , Dillen Josh , Hernandez Patrick , Czudnochowski Nadine , Cameroni Elisabetta , Beria Nicola , Ventresca Mariangela , Badellino Alberto , Lavorato-Hadjeres Soraya , Lecchi Elisabetta , Bonora Tecla , Mattiolo Matteo , Trinci Guido , Garzoni Daniela , Bonforte Giuseppe , Forni-Ogna Valentina , Giunzioni Davide , Berwert Lorenzo , Gupta Ravindra K. , Ferrari Paolo , Ceschi Alessandro , Cippà Pietro , Corti Davide , Lanzavecchia Antonio , Piccoli Luca
Published: October 2021

Patients on dialysis are at risk of severe course of SARS-CoV-2 infection. Understanding the neutralizing activity and coverage of SARS-CoV-2 variants of vaccine-elicited antibodies is required to guide prophylactic and therapeutic COVID-19 interventions in this frail population. By analyzing plasma samples from 130 hemodialysis and 13 peritoneal dialysis patients after two doses of BNT162b2 or mRNA-1273 vaccines, we found that 35% of the patients had low-level or undetectable IgG antibodies to SARS-CoV-2 Spike (S). Neutralizing antibodies against the vaccine-matched SARS-CoV-2 and Delta variant were low or undetectable in 49% and 77% of patients, respectively, and were further reduced against other emerging variants. The fraction of non-responding patients was higher in SARS-CoV-2-naïve hemodialysis patients immunized with BNT162b2 (66%) than those immunized with mRNA-1273 (23%). The reduced neutralizing activity correlated with low antibody avidity. Patients followed up to 7 months after vaccination showed a rapid decay of the antibody response with an average 21- and 10-fold reduction of neutralizing antibodies to vaccine-matched SARS-CoV-2 and Delta variant, which increased the fraction of non-responders to 84% and 90%, respectively. These data indicate that dialysis patients should be prioritized for additional vaccination boosts. Nevertheless, their antibody response to SARS-CoV-2 must be continuously monitored to adopt the best prophylactic and therapeutic strategy.
A Cross-sectional Comparison of Utilization of Medical Crowdfunding for Global Health
Authors: Siemens Andie , Rustja Samantha , Doiron R. Christopher , Siemens D. Robert
Published: October 2021

The online solicitation of public donations has become an important financing option for health care expenses, intensified by increasing costs and deficits of universal public systems (1). With growing internet access and success of the largest social crowdfunding platform, GoFundMe, online appeals for medical causes have grown significantly over the last decade in low-to high-income countries. The purpose of this study was to qualitatively describe the use of GoFundMe as a crowdfunding platform for global health initiatives given its supremacy in the social crowdfunding market. Three different cohorts (n=100 each) of online solicitation were examined as a cross-section comparing global health appeals to those for personal health care and animal activism. Variables included the purpose for crowdfunding, the characteristics of beneficiaries and campaigns, and the factors associated with funding success. Our cross-sectional review found that global health campaigns were focused on voluntourism opportunities compared to more specific, individualized appeals for those in need. Global health campaigns appeared to be the least ambitious and generally the least successful of those reviewed. Grouping the most and least successful campaigns between the different cohorts, global health appears to be more successful when targeting a larger population to donate smaller amounts of money and relying on sharing via social media. We suggest that compared to online solicitation for personal health and animal activism objectives, crowdfunding on GoFundMe has unrealized potential as a tool for global health initiatives. More work should be conducted using different crowdfunding platforms and a more longitudinal review in order to expand on these findings and their implications on health care provision in the countries examined. Furthermore, future inquiry is needed to understand the social and ethical implications of online solicitation for global health endeavors in order to inform policy and promote discussion around equity and accessibility.
Plant-pollinator specialization: Origin and measurement of curvature
Authors: Boehm Mannfred M.A. , Jankowski Jill E. , Cronk Quentin C.B.
Published: October 2021

A feature of biodiversity is the abundance of curves displayed by organs and organisms. Curvature is a widespread, convergent trait that has important ecological and evolutionary implications. In pollination ecology, the curvature of flowers and pollinator mouthparts (e.g. hummingbird bills) along the dorsiventral plane has been associated with specialization, competition, and species co-existence. Six methods have historically been used to measure curvature in pollination systems; we provide a solution to this inconsistency by defining curvature using well-established concepts from differential geometry. Intuitively, curvature is the degree to which a line is not straight, but more formally, it is the rate at which the tangent of a curve changes direction with respect to arc length. Here, we establish a protocol wherein a line is fitted against landmarks placed on an image of a curved organ or organism, then curvature is computed at many points along the fitted line and the sum taken. The protocol is demonstrated by studying the development of nectar spur curvature in the flowering plant genusEpimedium(Berberidaceae). By clarifying the definition of curvature, our aim is to make the language of comparative morphology more precise and broadly applicable to capture other curved structures in nature.
Immunogenicity of SARS-CoV-2 trimetric spike protein associated to Poly(I:C) plus Alum
Authors: dos-Santos Júlio Souza , Firmino-Cruz Luan , Fonseca-Martins Alessandra Marcia da , Oliveira-Maciel Diogo , Perez Gustavo Guadagini , Pereira Victor A. R. , Dumard Carlos H. , Guedes-da-Silva Francisca H. , Santos Ana C. Vicente , Leandro Monique dos Santos , Machado Ferreira Jesuino Rafael , Guimarães-Pinto Kamila , Conde Luciana , Rodrigues Danielle A. S. , de Mattos Silva Marcus Vinicius , Alvim Renata G. F. , Lima Tulio M. , Marsili Federico F. , Abreu Daniel P. B. , Ferreira Orlando , Borges Ronaldo da Silva Mohana , Tanuri Amilcar , Souza Thiago Moreno L. , Rossi-Bergamnn Bartira , Vale André M. , Silva Jerson Lima , de Oliveira Andrea Cheble , Filardy Alessandra D’Almeida , Gomes Andre M. O. , Leonel de Matos Guedes Herbert
Published: October 2021

The SARS-CoV-2 pandemic has had a social and economic impact worldwide, and vaccination is an efficient strategy for diminishing those damages. New adjuvant formulations are required for the high vaccine demands, especially adjuvant formulations that induce a Th1 phenotype. Herein we assess a vaccination strategy using a combination of Alum and polyinosinic:polycytidylic acid (Poly(I:C)) adjuvants plus the SARS-CoV-2 spike protein in a prefusion trimeric conformation by an intradermal (ID) route. We found high levels of IgG anti-spike antibodies in the serum by enzyme linked immunosorbent assay (ELISA) and high neutralizing titers against SARS-CoV-2in vitroby neutralization assay, after one or two boosts. By evaluating the production of IgG subtypes, as expected, we found that formulations containing Poly(I:C) induced IgG2a whereas Alum did not. The combination of these two adjuvants induced high levels of both IgG1 and IgG2a. In addition, cellular immune responses of CD4+and CD8+T cells producing interferon-gamma were equivalent, demonstrating that the Alum + Poly(I:C) combination supported a Th1 profile. Based on the high neutralizing titers, we evaluated B cells in the germinal centers, which are specific for receptor-binding domain (RBD) and spike, and observed that more positive B cells were induced upon the Alum + Poly(I:C) combination. Moreover, these B cells produced antibodies against both RBD and non-RBD sites. We also studied the impact of this vaccination preparation (spike protein with Alum + Poly(I:C)) in the lungs of mice challenged with inactivated SARS-CoV-2 virus. We found a production of IgG, but not IgA, and a reduction in neutrophil recruitment in the bronchoalveolar lavage fluid (BALF) of mice, suggesting that our immunization scheme reduced lung inflammation. Altogether, our data suggest that Alum and Poly(I:C) together is a possible adjuvant combination for vaccines against SARS-CoV-2 by the intradermal route.
The role of evolutionary modes for trait-based cascades in mutualistic networks
Authors: Bastazini Vinicius Augusto Galvão , Debastiani Vanderlei , Cappelatti Laura , Guimarães Paulo , Pillar Valério D.
Published: October 2021

The erosion of functional diversity may foster the collapse of ecological systems. Functional diversity is ultimately determined by the distribution of species traits. As species traits are a legacy of species evolutionary history, one might expect that the mode of trait evolution influences community resistance under the loss of functional diversity. In this paper, we investigate the role of trait evolutionary dynamics on the robustness of mutualistic networks undergoing the following scenarios of species loss: i) random extinctions, ii) loss of functional distinctiveness and iii) extinctions biased towards larger sizes. We simulated networks defined by models of single trait complementary and evolutionary modes where traits can arise in recent diversification events with weak phylogenetic signal, in early diversification events with strong phylogenetic signal, or as a random walk through evolutionary time. Our simulations show that mutualistic networks are especially vulnerable to extinctions based on trait distinctiveness and more robust to random extinction dynamics. The networks show an intermediate level of robustness against size-based extinctions. Despite the small range of variation in network robustness, our results show that the mode of trait evolution matters for network robustness in all three scenarios. Networks with low phylogenetic signal are more robust than networks with high phylogenetic signal across all scenarios. As a consequence, our results predict that mutualistic networks based upon current adaptations are more likely to cope with extinction dynamics than those networks that are based upon conserved traits.
Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area
Authors: Tognetti Marco , Sklodowski Kamil , Müller Sebastian , Kamber Dominique , Muntel Jan , Bruderer Roland , Reiter Lukas
Published: October 2021

The plasma proteome has the potential to enable a holistic analysis of the health state of an individual. However, plasma biomarker discovery is difficult due to its high dynamic range and variability. Here, we present a novel automated analytical approach for deep plasma profiling and applied it to a 180-sample cohort of human plasma from lung, breast, colorectal, pancreatic, and prostate cancer.

Using a controlled quantitative experiment, we demonstrate a 257% increase in protein identification and a 263% increase in significantly differentially abundant proteins over neat plasma.

In the cohort, we identified 2,732 proteins. Using machine learning, we discovered biomarker candidates such as STAT3 in colorectal cancer and developed models that classify the disease state. For pancreatic cancer, a separation by stage was achieved.

Importantly, biomarker candidates came predominantly from the low abundance region, demonstrating the necessity to deeply profile because they would have been missed by shallow profiling.
Cryo-EM structure of human Nup155 reveals the biochemical basis for atrial fibrillation linked genetic mutation R391H
Authors: Niranjan Sangeeta , Singh Jyotsana , Chauhan Radha
Published: October 2021

Human nuclear pore complexes are composed of ∼32 distinct nucleoporins to facilitate bidirectional nucleo-cytoplasmic transport. Many of them have been associated with various human diseases such as an inherited mutation (R391H) in Nup155 is shown as the clinical cause of atrial fibrillation and sudden cardiac arrest. Due to the lack of structural knowledge and mechanistic insights, the roles of Nups in NPC assembly and relevance in human diseases are very restricted. Here, we show the cryo-EM structure of human Nup155 at 5.2-5.7. Å resolution deciphered from 3 distinct particle classes: N-terminus (19-863), C-terminus (864-1337), and longer N-terminus (19-1069). It revealed intrinsic plasticity at the middle domain of Nup155 and the role of species-specific loop regions in an atypical 7-bladed β-propeller domain to provide a distinct interface for Nup93 and Nup35. Due to the proximity of these Nups interacting sites near the Arginine-391 position, atrial fibrillation linked genetic mutation (R391H) causes dissociation from NPC in absence of N-terminal 112 residues.

Highlights

Cryo-EM structure of human Nup155 at 5.2 Å resolution

Seven bladed β-propeller domain at N-terminus of Nup155 exhibited distinct features for interaction with Nup35 and Nup93

The middle domain of Nup155 is highly dynamic in nature

Structural mapping allows mechanistic interpretation of AF linked R391H mutation
Evidence of individual differences in motives for nicotine seeking in classical nicotine self-administration and associated outcomes of varenicline administration
Authors: Garcia-Rivas Vernon , Fiancette Jean-François , Tostain Jessica , de Maio Giulia , Wiart Jean-François , Gaulier Jean-Michel , Deroche-Gamonet Véronique
Published: October 2021

Abstract

Background

Smokers vary in their motives for tobacco seeking, suggesting that they could benefit from personalized treatments. However, these variations have received little attention in animal models for the study of tobacco dependence. In the most classically used model, ie. intravenous self-administration of nicotine in the rat, seeking behaviour is reinforced by the combination of intravenous nicotine with a discrete stimulus (eg. discrete cue light). In both human and animals, two types of psychopharmacological interactions between nicotine and environmental stimuli have been evidenced. Whether these two types of interactions contribute equally to nicotine seeking in all individuals is unknown.

Methods

We combined behavioural pharmacology and clustering analysis. In an outbred male rat population, we tested whether nicotine and the discrete nicotine-associated cue light contributed equally to self-administration in all individuals. Two clusters of rats were identified, in which we further studied the nature of the psychopharmacological interaction between nicotine and the cue, as well as the response to the cessation aid varenicline when nicotine was withdrawn.

Results

Notably, withdrawing nicotine produced drastic opposed effects on seeking behavior in the two identified clusters of rats; a 50% increase vs a 18% decrease, respectively. The first cluster of rats sought for the primary reinforcing effects of nicotine and the discrete cue light that has gained nicotine-like secondary reinforcing properties. The second cluster sought nicotine for its ability to enhance the primary reinforcing effects of the discrete cue light. Critically, the approved cessation aid Varenicline counteracted the absence of nicotine in both, but eventually decreasing seeking in the former but increasing it in the latter.

Conclusions

Classical rodent models for the study of the reinforcing and addictive effects of nicotine hide individual variations in the psychopharmacological motives supporting seeking behavior. These variations may be a decisive asset for improving their predictive validity in the perspective of precision medicine for smoking cessation.
Proteome-wide landscape of solubility limits in a bacterial cell
Authors: Györkei Ádám , Daruka Lejla , Balogh Dávid , Őszi Erika , Magyar Zoltán , Szappanos Balázs , Fekete Gergely , Fuxreiter Mónika , Horváth Péter , Pál Csaba , Kintses Bálint , Papp Balázs
Published: October 2021

Proteins are prone to aggregate when they are expressed above their solubility limits, a phenomenon termed supersaturation. Aggregation may occur as proteins emerge from the ribosome or after they fold and accumulate in the cell, but the relative importance of these two routes remain poorly known. Here, we systematically probed the solubility limits of each Escherichia coli protein upon overexpression using an image-based screen coupled with machine learning. The analysis suggests that competition between folding and aggregation from the unfolded state governs the two aggregation routes. Remarkably, the majority (70%) of insoluble proteins have low supersaturation risks in their unfolded states and rather aggregate after folding. Furthermore, a substantial fraction (∼35%) of the proteome remain soluble at concentrations much higher than those found naturally, indicating a large margin of safety to tolerate gene expression changes. We show that high disorder content and low surface stickiness are major determinants of high solubility and are favored in abundant bacterial proteins. Overall, our proteome-wide study provides empirical insights into the molecular determinants of protein aggregation routes in a bacterial cell.
Intracellular Delivery of Antibodies for Selective Cell Signaling Interference
Authors: Hershman Rebecca L. , Li Yamin , Ma Feihe , Xu Qioabing , Van Deventer James A.
Published: October 2021

Many intracellular signaling events remain poorly characterized due to a general lack of tools to interfere with “undruggable” targets. Antibodies have the potential to elucidate intracellular mechanisms via targeted disruption of cell signaling cascades because of their ability to bind to a target with high specificity and affinity. However, due to their size and chemical composition, antibodies cannot innately cross the cell membrane, and thus access to the cytosol with these macromolecules has been limited. Here, we describe strategies for accessing the intracellular space with recombinant antibodies mediated by cationic lipid nanoparticles to selectively disrupt intracellular signaling events. To enable such investigations, we first produced a series of antibody constructs, known as scFv-Fcs, containing additional, genetically encoded negative charges located at the C-termini of the constructs. Preparing proteins with negatively charged motifs has previously been shown to enhance intracellular protein delivery with cationic lipids, but usually for the purpose of genome editing or targeted cell death. We started by generating derivatives of scFv-Fc17, an antibody construct previously reported to bind specifically to signal transducer and activator of transcription 3 (STAT3) phosphorylated at Tyr705 (pYSTAT3). We screened a small number of lipids from our combinatorial lipid library with flow cytometry and found that PBA-Q76-O16B facilitated the most efficient delivery of scFv-Fcs under the conditions tested. In HepG2 cells, we observed up to 60.5% delivery efficacy, while in a STAT3-luciferase reporter cell line up to 71.5% delivery efficacy was observed. These results demonstrated the feasibility of accessing the intracellular space with scFv-Fcs. However, we also note that no more than modest changes were observed upon changing the numbers of negative charges in these constructs during delivery. Characterization of the cytotoxicity, size, and encapsulation efficiency of scFv-Fcs with PBA-Q76-O16B revealed that the constructs were generally well-behaved, with addition of differing quantities of negative charge resulting in at most modest effects. Importantly, functional assays monitoring transcriptional activity in luciferase reporter cell lines and HepG2 cells demonstrated significant reduction of gene expression downstream of pYSTAT3 following delivery of scFv-Fc17 constructs. Together, our results establish the use of recombinantly produced antibodies to selectively interfere with cell signaling events driven by a single posttranslational modification. Efficient intracellular delivery of engineered antibodies opens up possibilities for modulation of previously “undruggable” targets, including for potential therapeutic applications.
Intrinsic timescales as an organizational principle of neural processing across the whole rhesus macaque brain
Authors: Manea Ana M.G. , Zilverstand Anna , Uğurbil Kâmil , Heilbronner Sarah R. , Zimmermann Jan
Published: October 2021

Hierarchical temporal dynamics are a fundamental computational property of the brain; however, there are no whole-brain, noninvasive investigations into timescales of neural processing in animal models. To that end, we used the spatial resolution and sensitivity of ultrahigh field fMRI performed at 10.5 Tesla to probe timescales across the whole macaque brain. We uncovered within-species consistency between timescales estimated from fMRI and electrophysiology. Crucially, we extended existing electrophysiological hierarchies to whole brain topographies. Our results validate the complementary use of hemodynamic and electrophysiological intrinsic timescales, establishing a basis for future translational work. Further, with these results in hand, we were able to show that one facet of the high-dimensional functional connectivity topography of any region in the brain is closely related to hierarchical temporal dynamics. We demonstrated that intrinsic timescales are organized along spatial gradients that closely match functional connectivity gradient topographies across the whole brain. We conclude that intrinsic timescales are a unifying organizational principle of neural processing across the whole brain.

Declaration of Interests

The authors declare no competing interests.
SARS-CoV-2 RNA and antibody dynamics in a Dutch household study with dense sampling frame
Authors: Han Wanda G.H. , Swart Arno , Marinovic Axel Bonacic , Eggink Dirk , Reimerink Johan , Wijsman Lisa A. , van der Veer Bas , van den Brink Sharon , van den Brandt Anne-Marie , van Tol Sophie , Godeke Gert-Jan , Brouwer Fion , Hoogerwerf Marieke , Reukers Daphne F.M. , Rots Nynke , Reusken Chantal , Meijer Adam
Published: October 2021

This study investigated the dynamics of SARS-CoV-2 infection and diagnostics in household members of different ages and with different symptom severity after SARS-CoV-2 exposure during the early phase of the pandemic. Households with a SARS-CoV-2 confirmed positive case and at least one child in the Netherlands were followed for 6 weeks. Naso (NP)- and oropharyngeal (OP) swabs, oral fluid and feces specimens were analyzed for SARS-CoV-2 RNA and serum for SARS-CoV-2-specific antibodies. The dynamics of the presence of viral RNA and the serological response was modeled to determine the sampling time-frame and sample type with the highest sensitivity to confirm or reject a SARS-CoV-2 diagnosis. Transmission of SARS-CoV-2 between adults and children within a household was correlated with symptom severity of index cases. In children higher viral loads compared to adults were detected at symptom onset. Early in infection, higher viral loads were detected in NP and OP specimens, while RNA in especially feces were longer detectable. SARS-CoV-2-specific antibodies have a 90% probability of detection from 7 days (total Ig) and 18 days (IgG) since symptom onset. In conclusion this study has shown that on average, children carry higher loads of virus as compared to adults early after infection. For highest probability of detection in SARS-CoV-2 diagnostics early in infection, RT-PCR on NP and OP specimens are more sensitive than on oral fluid and feces. For SARS-CoV-2 diagnostics late after infection, RT-PCR on feces specimens and serology are more valuable.
Estimating the Efficacy of Common Treatments in Children and Young Adults Diagnosed with Cerebral Palsy Using Three Machine Learning Algorithms
Authors: Schwartz Michael H. , Ries Andrew J. , Georgiadis Andrew G.
Published: October 2021

Background

Orthopedic and neurological deformity are often treated in children and young adults with cerebral palsy (CP). Due to challenges arising from combinatorics, research funding priorities, and medical practicalities, the efficacy of these treatments is not well studied.

Objectives

Our goal was to estimate the efficacy of 13 common orthopedic and neurological treatments at four different levels of outcome in children and young adults diagnosed with CP. The outcome levels considered were anatomy and physiology, gait parameter, overall gait pattern, and function.

Methods

We used three well-establish causal inference approaches (direct matching, virtual twins, and Bayesian causal forests) and a large clinical gait analysis database to estimate the average treatment effect on the treated (ATT). We then examined the efficacy across treatments, methods, and outcome levels.

Results

The median ATT of 13 common treatments in children and young adults with CP, measured as Cohen’s D, bordered on medium at the anatomy and physiology level (median [IQR] = 0.42 [.05, .60]) and became smaller as we moved along the causal chain through gait parameter (0.21 [.01, .33]), overall gait pattern (0.09 [.03, .19]), and function (−0.01 [-.06, .13]).

Conclusions

Current treatments have medium effects on anatomy and physiology, but modest to minimal efficacy on gait and function. Further work is needed to understand the source of heterogeneous treatment effects, which are large in this patient population. Replication or refutation of these findings by other centers will be valuable to establish the generalizability of these results and for benchmarking of best practices.
Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions
Authors: Hasan Rahat , Humphrey Jack , Bettencourt Conceição , Lashley Tammaryn , Fratta Pietro , Raj Towfique
Published: October 2021

Frontotemporal lobar degeneration (FTLD) is a group of heterogeneous neurodegenerative disorders affecting the frontal and temporal lobes of the brain. Nuclear loss and cytoplasmic aggregation of the RNA-binding protein TDP-43 represents the major FTLD pathology, known as FTLD-TDP. To date, there is no effective treatment for FTLD-TDP due to an incomplete understanding of the molecular mechanisms underlying disease development. Here we compared post-mortem tissue RNA-seq transcriptomes from the frontal cortex, temporal cortex and cerebellum between 28 controls and 30 FTLD-TDP patients to profile changes in cell-type composition, gene expression and transcript usage. We observed downregulation of neuronal markers in all three regions of the brain, accompanied by upregulation of microglia, astrocytes, and oligodendrocytes, as well as endothelial cells and pericytes, suggesting shifts in both immune activation and within the vasculature. We validate our estimates of neuronal loss using neuropathological atrophy scores and show that neuronal loss in the cortex can be mainly attributed to excitatory neurons, and that increases in microglial and endothelial cell expression are highly correlated with neuronal loss. All our analyses identified a strong involvement of the cerebellum in the neurodegenerative process of FTLD-TDP. Altogether, our data provides a detailed landscape of gene expression alterations to help unravel relevant disease mechanisms in FTLD.
Deep Learning Model for Mortality Prediction of ICU Patients with Paralytic Ileus
Authors: Razo Martha , Pishgar Maryam , Darabi Houshang
Published: October 2021

Background

Paralytic Ileus (PI) patients in the Intensive Care Unit (ICU) are at a significant risk of death. Prediction of at-risk patients for mortality after 24 hours of admission of ICU PI patients is important to increase the life expectancy of PI patients.

Methods and Results

The proposed framework,DLMP(Deep Learning Model for Mortality Prediction of ICU Patients with PI) is a powerful deep learning model consisting of six total unique clinical lab items and two demographics as inputs to a Neural Network(NN) of only two neuron layers. Using the Medical Information Mart for Intensive Care III (MIMIC-III) dataset of 1,017 ICU PI patients, theDLMPresulted in the best prediction performance with an AUC score of 0.866.

Conclusion

The proposed approach is capable of modeling the mortality of ICU patients after 24 hours admission using only six unique total clinical data and two demographics with a simple NN architecture.DLMPframework significantly improves the outcome prediction compared to the process mining and machine learning models. The proposedDLMPhas the potential of allowing clinicians to create targeted interventions that reduce mortality for PI patients in an ICU setting.
Optimizing the live attenuated influenza A vaccine backbone for high-risk patient groups
Authors: Bonifacio João P.P. , Williams Nathalia , Garnier Laure , Hugues Stephanie , Schmolke Mirco , Mazel-Sanchez Beryl
Published: October 2021

The live attenuated influenza vaccine (LAIV) is approved for intranasal spray application in 2-49 year-old patients with safety concerns limiting its use in younger children and immunocompromised patients, mainly from the higher incidence of adverse events and the possibility of uncontrolled replication and reversion to a pathogenic strain, respectively. Further attenuation of the LAIV could generally improve its safety profile, which might come at the cost of reduced immunogenicity. To solve this dilemma, we took advantage of a recently defined mechanism of ER stress induction by modifying IAV non-structural protein 1 (NS1). The modified LAIV (AAmut/PR8) showed stronger ER stress activation in vitro and replicated to lower titers in vivo compared to its parental strain, without affecting protection against homo-subtypic or hetero-subtypic IAV strains. AAmut/PR8 could pose as a suitable strategy to attend the gap to the current LAIV recommendation guidelines in susceptible target populations.
Neutral competition explains the clonal composition of neural organoids
Authors: Pflug Florian G. , Haendeler Simon , Esk Christopher , Lindenhofer Dominik , Knoblich Jürgen A. , von Haeseler Arndt
Published: October 2021

Cerebral organoids model the development of the human brain and are an indispensable tool for studying neurodevelopment. Whole-organoid lineage tracing has revealed the number of progeny arising from each initial stem cell to be highly diverse, with lineage sizes ranging from one to more than 20,000 cells. This exceeds what can be explained by existing stochastic models of corticogenesis, indicating the existence of an additional source of stochasticity. We propose an explanation in terms of the SAN model in which this additional source of stochasticity is the survival time of a lineage within a long-lived population of symmetrically dividing cells under neutral competition. We demonstrate that this model explains the experimentally observed variability of lineage sizes and we derive a formula that captures the quantitative relationship between survival time and lineage size. Finally, we show that our model implies the existence of a regulatory mechanism to keeps the size of the symmetrically dividing cell population constant.
Selective modulation of cell surface proteins during vaccinia infection: implications for immune evasion strategies
Authors: Depierreux Delphine M , Altenburg Arwen F , Soday Lior , Fletcher-Etherington Alice , Anthrobus Robin , Ferguson Brian J , Weekes Michael P , Smith Geoffrey L
Published: October 2021

The interaction between immune cells and virus-infected targets involves multiple plasma membrane (PM) proteins. A systematic study of PM protein modulation by vaccinia virus (VACV), the paradigm of host regulation, has the potential to reveal not only novel viral immune evasion mechanisms, but also novel factors critical in host immunity. Here, >1000 PM proteins were quantified throughout VACV infection, revealing selective downregulation of known T and NK cell ligands including HLA-C, downregulation of cytokine receptors including IFNAR2, IL-6ST and IL-10RB, and rapid inhibition of expression of certain protocadherins and ephrins, candidate activating immune ligands. Downregulation of most PM proteins occurred via a proteasome-independent mechanism. Upregulated proteins included a decoy receptor for TRAIL. Twenty VACV-encoded PM proteins were identified, of which five were not recognised previously as such. Collectively, this dataset constitutes a valuable resource for future studies on antiviral immunity, host-pathogen interaction, poxvirus biology, vector-based vaccine design and oncolytic therapy.
A Helicase-tethered ORC Flip Enables Bidirectional Helicase Loading
Authors: Gupta Shalini , Friedman Larry J. , Gelles Jeff , Bell Stephen P.
Published: October 2021

Replication origins are licensed by loading two Mcm2-7 helicases around DNA in a head-to-head conformation poised to initiate bidirectional replication. This process requires ORC, Cdc6, and Cdt1. Although different Cdc6 and Cdt1 molecules load each helicase, whether two ORC proteins are required is unclear. Using colocalization single-molecule spectroscopy combined with FRET, we investigated interactions between ORC and Mcm2-7 during helicase loading. We demonstrate that a single ORC molecule can recruit both Mcm2-7/Cdt1 complexes via similar interactions that end upon Cdt1 release. Between the first and second helicase recruitment, we observe a rapid change in interactions between ORC and the first Mcm2-7. In quick succession ORC breaks the interactions mediating first Mcm2-7 recruitment, releases from its initial DNA-binding site, and forms a new interaction with the opposite face of the first Mcm2-7. This rearrangement requires release of the first Cdt1 and tethers ORC as it flips over the first Mcm2-7 to form an inverted Mcm2-7-ORC-DNA complex required for second-helicase recruitment. To ensure correct licensing, this complex is maintained until head-to-head interactions between the two helicases are formed. Our findings reconcile previous observations and reveal a highly-coordinated series of events through which a single ORC molecule can load two oppositely-oriented helicases.
Highly concentrated trehalose induces transient senescence-associated secretory phenotype in fibroblasts via CDKN1A/p21
Authors: Muto Jun , Fukuda Shinji , Watanabe Kenji , Dai Xiuju , Tsuda Teruko , Kiyoi Takeshi , Mori Hideki , Shiraishi Ken , Murakami Masamoto , Higashiyama Shigeki , Mizukami Yoichi , Sayama Koji
Published: October 2021

Trehalose is the nonreducing disaccharide of glucose, evolutionarily conserved in invertebrates, but does not exist in vertebrates. The living skin equivalent (LSE) is an organotypic coculture containing keratinocytes cultivated on fibroblast-populated dermal substitutes. We demonstrated that human primary fibroblasts treated with highly concentrated trehalose promote significantly extensive spread of the epidermal layer of LSE without any deleterious effects. The RNA-seq analysis data and Ingenuity pathway analysis of the differentially expressed genes of trehalose-treated 2D and 3D fibroblasts at early time points revealed the involvement of the CDKN1A pathway, which is necessary for the marked upregulation of growth factors including DPT. By contrast, the mRNA-seq data of LSEs 2-weeks after air exposure indicated that gene expression profiles are similar for untreated and trehalose-treated cells in both keratinocytes and fibroblasts. The trehalose-treated fibroblasts were positive for senescence-associated β-galactosidase with the significantly downregulated expressions of LMNB1. Finally, we demonstrated that transplantation of the dermal substitute with trehalose-treated fibroblasts accelerated wound closure and increased capillary formation significantly in the experimental mouse woundsin vivo. These data indicate that high-concentration trehalose can induce the beneficial senescence-associated secretory phenotype in fibroblasts via CDKN1A/p21, which may be therapeutically useful for optimal wound repair.
Transcript accumulation rates in the earlyCaenorhabditis elegansembryo
Authors: Sivaramakrishnan Priya , Watkins Cameron , Murray John Isaac
Published: October 2021

Dynamic changes in transcription are widespread in developing embryos, where cell cycles are rapid and cell fate decisions need to be made quickly, often before the next cell division. Some fate decisions in the earlyCaenorhabditis elegansembryo overcome these constraints through the rapid production of high absolute levels of transcription factor mRNAs. Single cell accumulation rates for a small subset of developmental genes are known, but genome-scale measurements are lacking. Furthermore, how different aspects of transcription kinetics are fine-tuned for different genes to achieve the appropriate RNA levels is still being worked out. We describe a novel strategy to analyze single cell RNA sequencing data from the earlyC. elegansembryo. We estimate the absolute accumulation rates of zygotic genes up to the 16-cell stage and calibrate predicted rates with single molecule transcript imaging. We show that rapid transcript accumulation is common across different cell types and lineages and rates are the highest soon after zygotic transcription begins. High-rate transcription is a characteristic of genes encoding transcription factors with functions in cell fate specification. These genes share common genomic features and are more likely to have undergone recent duplication. We identify core promoter motifs that might drive high absolute RNA accumulation rates. We measured the contributions of core promoter elements to accumulation rate for one rapidly accumulating gene,ceh-51, which is required for mesoderm development. We find that mutating individual motifs modestly decreases the accumulation rate ofceh-51mRNA, suggesting multifactorial control of transcript accumulation rates. These results are a step towards estimating absolute transcription kinetics during embryonic fate specification and understanding how transcript dosage drives developmental decisions.