bluuebunny/crossref_metadata_2025 huggingface dataset:
RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity
Authors: Angioni R. , Bonfanti M. , Caporale N. , Sánchez-Rodríguez R. , Munari F. , Savino A. , Buratto D. , Pagani I. , Bertoldi N. , Zanon C. , Ferrari P. , Ricciardelli E. , Putaggio C. , Ghezzi S. , Elli F. , Rotta L. , Iorio F. , Zonta F. , Cattelan A. , Vicenzi E. , Molon B. , Villa C.E. , Viola A. , Testa G.
Published: May 2022

The spread of SARS-CoV-2 has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges due to subsequent waves and long-term consequences of great concern. Here we charted the molecular basis of COVID-19 pathogenesis, by analysing patients’ immune response at single-cell resolution across disease course and severity. This approach uncovered cell subpopulation-specific dysregulation in COVID-19 across disease course and severity and identified a severity-associated activation of the receptor for advanced glycation endproduct (RAGE) pathway in monocytes.In vitroexperiments confirmed that monocytes bind the SARS-CoV-2 S1-RBD via RAGE and that RAGE-Spike interactions drive monocyte infection. Our results demonstrate that RAGE is a novel functional receptor of SARS-CoV-2 contributing to COVID-19 severity.

One-Sentence Summary

Monocyte SARS-CoV-2 infection via the receptor for advanced glycation endproduct triggers severe COVID-19.
Post-covid medical complaints after SARS-CoV-2 Omicron vs Delta variants - a prospective cohort study
Authors: Magnusson Karin , Kristoffersen Doris Tove , Dell’Isola Andrea , Kiadaliri Ali , Turkiewicz Aleksandra , Runhaar Jos , Bierma-Zeinstra Sita , Englund Martin , Magnus Per Minor , Kinge Jonas Minet
Published: May 2022

Objective

To examine whether persons infected with the SARS-CoV-2 omicron variant have an altered risk of post-covid complaints and healthcare use when compared to 1) persons testing negative, and 2) persons with delta.

Design

Prospective cohort study with 126 days follow-up and a time-to-event approach.

Setting

A registry-based study including Norwegian residents.

Participants

All persons aged 18-70 years living in Norway and who had a negative polymerase chain reaction (PCR) test for SARS-CoV-2 (N=105 196, mean (SD) age 42 (14), 50% women)) or positive test with confirmed omicron variant (N=13 028, mean (SD) age 37 (13), 50% women) or delta variant (N=23 368, mean (SD) age 40 (12), 50% women) in December 2021. Individuals with hospital contacts or non-screened PCR test were excluded.

Main outcome measures

Symptoms/complaints and diagnosis of musculoskeletal pain, fatigue, cough, heart palpitations, shortness of breath, anxiety/depression and brain fog at the general practitioner or emergency ward as recorded in national registries and as observed for the whole follow-up period as well as in periods 14-30 days, 30-90 days and 90 days or more.

Results

Persons with omicron or delta had similarly increased risk of post-covid fatigue compared to persons testing negative, with a hazard ratio (HR)=1.21 (CI:1.10-1.33) for omicron and HR=1.26 (CI: 1.17-1.35) for delta, for up to 126 days after the test date. They also had an increased risk of shortness of breath (HR=1.43, CI, 1.14-1.80 and HR=1.70, CI, 1.46-1.98 for omicron and delta, respectively, relative to negative). Omicron was related with a similar, and no increased risk of musculoskeletal pain, cough, heart palpitations, anxiety/depression when compared to delta and when compared to test negative. The risk of complaints was similar for omicron and delta and decreased over time for the post-covid periods 14-30 days, 30-90 days and 90 days or more.

Conclusions

SARS-CoV-2 omicron and delta infection are associated with similarly increased risks of post-covid complaints when compared to non-infected. The omicron variant will likely lead to a temporarily increased burden on healthcare services.
Comparison of cardiovascular and renal outcomes between dapagliflozin and empagliflozin in patients with type 2 diabetes
Authors: Lim Jayoung , Hwang In-Chang , Choi Hong-Mi , Yoon Yeonyee E. , Cho Goo-Yeong
Published: May 2022

Background

The cardiovascular and renal benefits of sodium glucose co-transporter 2 inhibitors (SGLT2i) have been clearly demonstrated. However, studies comparing the effects of dapagliflozin and empagliflozin are scarce. Therefore, we aimed to compare the clinical outcomes between dapagliflozin and empagliflozin in patients with type 2 diabetes without prior atherosclerotic cardiovascular disease, chronic kidney disease, or heart failure.

Methods

Using a propensity-score matching method, we retrospectively analyzed 921 patients treated with dapagliflozin, 921 patients treated with empagliflozin, and 1842 patients treated with dipeptidyl peptidase-4 inhibitors (DPP4i; control group). Study outcomes comprised composite coronary events (acute coronary syndrome and coronary revascularization), composite ischemic events (coronary events and stroke), and composite heart failure and renal events.

Results

During follow up (median, 43.4 months), the incidence of composite coronary events was significantly lower in the SGLT2i groups than in the control group, and the incidence of composite ischemic events was lower in the dapagliflozin group than in the control group. Dapagliflozin and empagliflozin both demonstrated significant benefits in terms of heart failure and renal outcomes, supported by renoprotective effects, as assessed by the change in glomerular filtration rate. At 24–36 months of treatment, the empagliflozin group had higher low-density lipoprotein cholesterol levels, and lower glycated hemoglobin levels, compared to those in the dapagliflozin and control groups.

Conclusion

SGLT2i use was associated with a significantly reduced risk of atherosclerotic cardiovascular events, heart failure hospitalization, and renal events, compared to that with DPP4i use. There were no significant differences in clinical outcomes between dapagliflozin and empagliflozin, supporting a SGLT2i class effect.
Spontaneous object exploration in a recessive gene knockout model of Parkinson’s disease: Development and progression of object recognition memory deficits in male Pink1-/- rats
Authors: Pinizzotto Claudia C. , Dreyer Katherine M. , Aje Oluwagbohunmi A. , Caffrey Ryan M. , Madhira Keertana , Kritzer Mary F
Published: May 2022

Cognitive impairments appear at or before motor signs in about one third of patients with Parkinson’s disease (PD) and have a cumulative prevalence of roughly 80% overall. These deficits exact an unrelenting toll on patients’ quality and activities of daily life due in part to a lack of available treatments to ameliorate them. This study used three well-validated novel object recognition-based paradigms to explore the suitability of rats with knockout of the PTEN-induced putative kinase1 gene (Pink1) for investigating factors that induce cognitive decline in PD and for testing new ways to mitigate them. Longitudinal testing of rats from three to nine months of age revealed significant impairments in male Pink1-/- rats compared to wild type controls in Novel Object Recognition, Novel Object Location and Object-in-Place tasks. Task-specific differences in the progression of object discrimination/memory deficits across age were also seen. Finally, testing using an elevated plus maze, a tapered balance beam and a grip strength gauge showed that in all cases recognition memory deficits preceded potentially confounding impacts of gene knockout on affect or motor function. Taken together, these findings suggest that knockout of the Pink1 gene negatively impacts the brain circuits and/or neurochemical systems that support performance in object recognition tasks. Further investigations using Pink1-/-rats and object recognition memory tasks should provide new insights into the neural underpinnings of the visual recognition memory and visuospatial information processing deficits that are often seen in PD patients and accelerate the pace of discovery of better ways to treat them.
An Approach for Estimating Explanation Uncertainty in fMRI dFNC Classification
Authors: Ellis Charles A. , Miller Robyn L. , Calhoun Vince D.
Published: May 2022

In recent years, many neuroimaging studies have begun to integrate gradient-based explainability methods to provide insight into key features. However, existing explainability approaches typically generate a point estimate of importance and do not provide insight into the degree of uncertainty associated with explanations. In this study, we present a novel approach for estimating explanation uncertainty for convolutional neural networks (CNN) trained on neuroimaging data. We train a CNN for classification of individuals with schizophrenia (SZs) and controls (HCs) using resting state functional magnetic resonance imaging (rs-fMRI) dynamic functional network connectivity (dFNC) data. We apply Monte Carlo batch normalization (MCBN) and generate an explanation following each iteration using layer-wise relevance propagation (LRP). We then examine whether the resulting distribution of explanations differs between SZs and HCs and examine the relationship between MCBN-based LRP explanations and regular LRP explanations. We find a number of significant differences in LRP relevance for SZs and HCs and find that traditional LRP values frequently diverge from the MCBN relevance distribution. This study provides a novel approach for obtaining insight into the level of uncertainty associated with gradient-based explanations in neuroimaging and represents a significant step towards increasing reliability of explainable deep learning methods within a clinical setting.
Image-to-image generative adversarial networks for synthesizing perfusion parameter maps from DSC-MR images in cerebrovascular disease
Authors: Kossen Tabea , Madai Vince I , Mutke Matthias A , Hennemuth Anja , Hildebrand Kristian , Behland Jonas , Hilbert Adam , Sobesky Jan , Bendszus Martin , Frey Dietmar
Published: May 2022

Stroke is a major cause for death or disability. As imaging based patient stratification improves acute stroke therapy, dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) is is of major interest to image brain perfusion. However, expert-level perfusion maps require a manual or semi-manual post-processing by a medical expert making the procedure time-consuming and less standardized. Modern machine learning methods such as generative adversarial networks (GANs) have the potential to automate the perfusion map generation on an expert-level without manual validation. We propose a modified pix2pix GAN with a temporal component (temp-pix2pix-GAN) that generates perfusion maps in an end-to-end fashion. We train our model on perfusion maps infused with expert knowledge to encode it into the GANs. The performance was trained and evaluated using the structural similarity index measure (SSIM) on two datasets including acute stroke patients and patients with steno-occlusive disease. Our temp-pix2pix architecture showed high performance on the acute stroke dataset for all perfusion maps (mean SSIM 0.92-0.99) and good performance on data including patients with steno-occlusive disease (mean SSIM 0.84-0.99). While clinical validation is still necessary in future studies, our results mark an important step towards automated expert-level perfusion maps and thus, fast patient stratification.
Individual brain regulation as learned via neurofeedback is related to affective changes in adolescents with autism spectrum disorder
Authors: Klöbl Manfred , Prillinger Karin , Diehm Robert , Doganay Kamer , Lanzenberger Rupert , Poustka Luise , Plener Paul , Konicar Lilian
Published: May 2022

Background

Even though emotions often play a role in neurofeedback (NF) regulation strategies, investigations of the relationship between the induced neuronal changes and improvements in affective domains are scare in electroencephalography-based studies. We thus extend the findings of the first study on slow cortical potential (SCP) NF in autism spectrum disorder (ASD) by relating affective changes to whole-brain activity at rest and during regulation.

Methods

Forty-one male adolescents with ASD were scanned at rest using functional magnetic resonance imaging before and after half of them underwent NF training and half received treatment as usual. Furthermore, parents reported on affective characteristics at both times. The NF group had to alternatingly produce negative and positive SCP during training and was additionally scanned while applying their developed regulation strategies.

Results

We did not find significant treatment group-by-time interactions in affective or resting-state measures. However, we found increases of resting activity in the anterior cingulate cortex and right inferior temporal gyrus as well as improvements in affective characteristics over both groups. Activation corresponding to SCP differentiation in these regions correlated with the affective improvements. A further correlation was found for Rolandic operculum activation corresponding to positive SCP shifts. There were no significant correlations with the respective achieved SCP regulation during NF training.

Conclusion

SCP NF in ASD did not lead to superior improvements in neuronal or affective functioning compared to treatment as usual. However, the affective changes might be related to the individual strategies and their corresponding activation patterns as indicated by significant correlations on the whole-brain level but not the achieved SCP regulation.

Trial registration

This clinical trial was registered at drks.de (DRKS00012339) on 20thApril, 2017.
Social Frailty Index: Development and Validation of an Index of Social Attributes Predictive of Mortality in Older Adults
Authors: Shah Sachin J , Oreper Sandra , Jeon Sun Young , Boscardin W. John , Fang Margaret , Covinsky Kenneth E
Published: May 2022

Objective

To develop and validate the Social Frailty Index, a summary measure of social risk in older adults, and determine its ability to risk stratify beyond traditional medical risk models

Design

Prognostic model development and validation using demographics and a comprehensive inventory of social characteristics

Setting

The Health and Retirement Study, a longitudinal, nationally representative survey of U.S. adults >50 years. We developed the model using the 2010 wave and validated it using the 2012 wave; there was no overlap between 2010 and 2012 respondents.

Participants

8250 adults aged ≥65 years who completed the Psychosocial and Lifestyle Questionnaire (4302 in the 2010 development cohort, 3948 in the 2012 validation cohort).

Main exposure

Demographic and social characteristics

Main outcome

4-year mortality

Results

Within 4 years of the baseline interview, 22% of study participants in both the development and validation cohort had died. Drawn from 183 possible predictors, the final model included age, gender, and 8 social predictors: lacking neighborhood cleanliness, low perceived control over financial situation, having children and meeting with them less than yearly, not working for pay, less active with children (grandchildren, neighborhood, nieces/nephews), no volunteering or charity work, feeling isolated from others, being treated with less courtesy or respect. In the validation cohort, the model discriminated well (c-statistic 0.73) and was strongly associated with 4-year mortality (7.3% in the lowest decile, 59.9% in the highest decile). Also, the Social Frailty Index meaningfully risk-stratified participants beyond the Charlson score, a commonly used medical comorbidity index, and the Lee Index score, a comorbidity and function model.

Conclusion

This prognostic index, which includes age, gender, and 8 social characteristics, accurately risk stratifies older adults and refines the prediction of commonly used comorbidity- and function-based risk models.
Gut Microbes and the Liver Circadian Clock Partition Glucose and Lipid Metabolism
Authors: Frazier Katya , Manzoor Sumeed , Carroll Katherine , DeLeon Orlando , Miyoshi Sawako , Miyoshi Jun , George Marissa St , Tan Alan , Izumo Mariko , Takahashi Joseph S. , Rao Mrinalini C. , Leone Vanessa A. , Chang Eugene B.
Published: May 2022

Circadian rhythms govern glucose homeostasis, and their dysregulation leads to complex metabolic diseases. Gut microbes also exhibit diurnal rhythms that influence host circadian networks and metabolic processes, yet underlying mechanisms remain elusive. Here, we show hierarchical, bi-directional communication between the liver circadian clock, gut microbes, and glucose homeostasis in mice. The liver clock, but not the forebrain clock, requires gut microbes to drive glucose clearance and gluconeogenesis. Liver clock dysfunctionality expands proportions and abundances of oscillating microbial features by two-fold relative to controls. The liver clock is the primary driver of differential and rhythmic hepatic expression of glucose and fatty acid metabolic pathways. Absent the liver clock, gut microbes provide secondary cues that dampen these rhythms, resulting in reduced utilization of lipids as fuel relative to carbohydrates. Together, the liver clock transduces signals from gut microbes necessary to regulate glucose and lipid metabolism and meet energy demands over 24 hours.

Highlights

The liver circadian clock is autonomous from the central clock in metabolic regulation

Liver clock and gut microbes interact to direct hepatic glucose and lipid metabolism

Reciprocating host-microbe interactions drive rhythmic hepatic transcription

Perturbed liverBmal1results in chaotic downstream oscillators and metabolism
Functional analysis of PsbS transmembrane domains through base editing in Physcomitrium patens
Authors: Beraldo Claudia , Guyon-Debast Anouchka , Alboresi Alessandro , Nogué Fabien , Morosinotto Tomas
Published: May 2022

Plants exposed to light fluctuations are protected from photodamage by non-photochemical quenching (NPQ), a reversible mechanism that enables dissipation of excess absorbed energy as heat, which is essential for plant fitness and crop productivity. NPQ requires the activity of the membrane protein PsbS that, upon activation, interacts with antenna proteins, inducing their dissipative conformation. Here, we exploited base editing in the moss Physcomitrium patens to introduce in vivo specific amino acid changes and assess their impact on PsbS activity, targeting transmembrane regions to investigate their role in protein–protein interactions. This approach enabled the recognition of residues essential for protein stability and the identification of a hydrophobic cluster of amino acids with a seminal role in PsbS activity. This work provides new information on the PsbS molecular mechanism while also demonstrating the potential of base editing approaches for in planta gene function analysis.
Alcohol reverses the effects ofKCNJ6(GIRK2) noncoding variants on excitability of human glutamatergic neurons
Authors: Popova Dina , Gameiro-Ros Isabel , Youssef Mark M. , Zalamea Petronio , Morris Ayeshia D. , Prytkova Iya , Jadali Azadeh , Kwan Kelvin Y. , Kamarajan Chella , Salvatore Jessica E. , Xuei Xiaoling , Chorlian David B. , Porjesz Bernice , Kuperman Samuel , Dick Danielle M. , Goate Alison , Edenberg Howard J. , Tischfield Jay A. , Pang Zhiping P. , Slesinger Paul A. , Hart Ronald P.
Published: May 2022

Synonymous and noncoding single nucleotide polymorphisms (SNPs) in theKCNJ6gene, encoding G protein-gated inwardly rectifying potassium (GIRK2) channel subunit 2, have been linked with increased electroencephalographic frontal theta event-related oscillations (ERO) in subjects diagnosed with alcohol use disorder (AUD). To identify molecular and cellular mechanisms while retaining the appropriate genetic background, we generated induced excitatory glutamatergic neurons (iN) from iPSCs derived from four AUD-diagnosed subjects withKCNJ6variants (‘Affected: AF’) and four control subjects without variants (‘Unaffected: UN’). Neurons were analyzed for changes in gene expression, morphology, excitability and physiological properties. Single cell RNA sequencing suggests thatKCNJ6AF variant neurons have altered patterns of synaptic transmission and cell projection morphogenesis. Results confirm that AF neurons express lower levels of GIRK2, have greater neurite area, and elevated excitability. Interestingly, exposure to intoxicating concentrations of ethanol induces GIRK2 expression and reverses functional effects in AF neurons. Ectopic overexpression of GIRK2 alone mimics the effect of ethanol to normalize induced excitability. We conclude thatKCNJ6variants decrease GIRK2 expression and increase excitability and that this effect can be minimized or reduced with ethanol.
High-fidelity reproduction of visual signals by electrical stimulation in the central primate retina
Authors: Gogliettino Alex R. , Madugula Sasidhar S. , Grosberg Lauren E. , Vilkhu Ramandeep S. , Brown Jeff , Nguyen Huy , Kling Alexandra , Hottowy Paweł , Dąbrowski Władysław , Sher Alexander , Litke Alan M. , Chichilnisky E.J.
Published: May 2022

Electrical stimulation of retinal ganglion cells (RGCs) with electronic implants provides rudimentary artificial vision to people blinded by retinal degeneration. However, current devices stimulate indiscriminately and therefore cannot reproduce the intricate neural code of the retina. Recent work has demonstrated more precise activation of RGCs using focal electrical stimulation with multi-electrode arrays in the peripheral macaque retina, but it is unclear how effective this can be in the central retina, which is required for high-resolution vision. This work probes the neural code and effectiveness of focal epiretinal stimulation in the central macaque retina, using large-scale electrical recording and stimulationex vivo. The functional organization, light response properties, and electrical properties of the major RGC types in the central retina were mostly similar to the peripheral retina, with some notable differences in density, kinetics, linearity, spiking statistics and correlations. The major RGC types could be distinguished by their intrinsic electrical properties. Electrical stimulation targeting parasol cells revealed similar activation thresholds and reduced axon bundle activation in the central retina, but lower stimulation selectivity. Quantitative evaluation of the potential for image reconstruction from electrically-evoked parasol cell signals revealed higher overall expected image quality in the central retina. An exploration of inadvertent midget cell activation suggested that it could contribute high spatial frequency noise to the visual signal carried by parasol cells. These results support the possibility of reproducing high-acuity visual signals in the central retina with an epiretinal implant.

Significance Statement

Artificial restoration of vision with retinal implants is a major treatment for blindness. However, present-day implants do not provide high-resolution visual perception, in part because they do not reproduce the natural neural code of the retina. Here we demonstrate the level of visual signal reproduction that is possible with a future implant by examining how accurately responses to electrical stimulation of parasol retinal ganglion cells (RGCs) can convey visual signals. Although the precision of electrical stimulation in the central retina was diminished relative to the peripheral retina, the quality of expected visual signal reconstruction in parasol cells was greater. These findings suggest that visual signals could be restored with high fidelity in the central retina using a future retinal implant.
Hemin shows antiviral activity in vitro, possibly through suppression of viral entry mediators
Authors: Unal Mehmet Altay , Bitirim Ceylan Verda , Somers Julia , Summak Gokce Yagmur , Besbinar Omur , Kocakaya Ebru , Gurcan Cansu , Nazir Hasan , Aksoy Ozer Zeynep Busra , Ozkan Sibel Aysil , Bereketoglu Sidar , Ozkul Aykut , Demir Emek , Akcali Kamil Can , Yilmazer Acelya
Published: May 2022

Heme oxygenase-1 (HO-1) is a stress-induced enzyme that catalyzes the breakdown of heme into biliverdin, carbon monoxide, and iron. Targeting HO-1 to treat severe COVID-19 has been suggested by several groups, yet the role of HO-1 in SARS-CoV-2 infection remains unclear. Based on this, we aimed to investigate the antiviral activity of Hemin, an activator of HO-1. Infectivity of SARS-CoV-2 was decreased in Vero E6 cells treated with Hemin. Hemin also decreased TMPRSS2 and ACE2 mRNA levels in non-infected cells, possibly explaining the observed decrease in infectivity. TMPRSS2 protein expression and proteolytic activity were decreased in Vero E6 cells treated with Hemin. Besides that, experimental studies supported with in silico calculations. Overall, our study supports further exploration of Hemin as a potential antiviral and inflammatory drug for the treatment of COVID-19.
SPIRAL: Significant Process InfeRence ALgorithm for single cell RNA-sequencing and spatial transcriptomics
Authors: Biran Hadas , Hashimshony Tamar , Mandel-Gutfreund Yael , Yakhini Zohar
Published: May 2022

1

Gene expression data is complex and may hold information regarding multiple biological processes at once. We present SPIRAL, an algorithm that uses a Gaussian statistical model to produce a comprehensive overview of a plurality of significant processes detected in single cell RNA-seq or spatial transcriptomics data. SPIRAL identifies biological processes by finding sub-matrices that consist of the subset of genes involved and the subset of cells or spots. We describe the algorithmic method, the analysis pipeline and several example results. SPIRAL is available athttps://spiral.technion.ac.il/.
Chemical effects on ecological interactions within a model-experiment loop
Authors: Lamonica Dominique , Charles Sandrine , Clément Bernard , Lopes Christelle
Published: May 2022

We propose in this paper a method to assess the effects of a contaminant on a micro-ecosystem, integrating the population dynamics and the interactions between species. For that, we developed a dynamic model to describe the functioning of a microcosm exposed to a contaminant and to discriminate direct and indirect effects. Then, we get back from modelling to experimentation in order to identify which of the collected data have really been necessary and sufficient to estimate model parameters in order to propose a more efficient experimental design for further investigations. We illustrated our approach using a 2-L laboratory microcosm involving three species (the duckweedLemna minor, the microalgaePseudokirchneriella subcapitataand the daphnidsDaphnia magna) exposed to cadmium contamination. We modelled the dynamics of the three species and their interactions using a mechanistic model based on coupled ordinary differential equations. The main processes occurring in this three-species microcosm were thus formalized, including growth and settling of algae, growth of duckweeds, interspecific competition between algae and duckweeds, growth, survival and grazing of daphnids, as well as cadmium effects. We estimated model parameters by Bayesian inference, using simultaneously all the data issued from multiple laboratory experiments specifically conducted for this study. Cadmium concentrations ranged between 0 and 50μg.L-1. For all parameters of our model, we obtained biologically realistic values and reasonable uncertainties. The cascade of cadmium effects, both direct and indirect, was identified. Critical effect concentrations were provided for the life history traits of each species. An example of experimental design adapted to this kind a microcosm was also proposed. This approach appears promising when studying contaminant effects on ecosystem functioning.
HyperVR–A hybrid prediction framework for virulence factors and antibiotic resistance genes in microbial data
Authors: Ji Boya , Pi Wending , Zhang Xianglilan , Peng Shaoliang
Published: May 2022

Infectious diseases, particularly bacterial infections, are emerging at an unprecedented rate, posing a serious challenge to public health and the global economy. Different virulence factors (VFs) work in concert to enable pathogenic bacteria to successfully adhere, reproduce and cause damage to host cells, and antibiotic resistance genes (ARGs) allow pathogens to evade otherwise curable treatments. To understand the causal relationship between microbiome composition, function and disease, both VFs and ARGs in microbial data must be identified. Most existing computational models cannot simultaneously identify VFs or ARGs, hindering the related research. The best hit approaches are currently the main tools to identify VFs and ARGs concurrently; yet they usually have high false-negative rates and are very sensitive to the cut-off thresholds. In this work, we proposed a hybrid computational framework called HyperVR to predict VFs and ARGs at the same time. Specifically, HyperVR integrates key genetic features and then stacks classical ensemble learning methods and deep learning for training and prediction. HyperVR accurately predicts VFs, ARGs and negative genes (neither VFs nor ARGs) simultaneously, with both high precision (>0.91) and recall (>0.91) rates. Also, HyperVR keeps the flexibility to predict VFs or ARGs individually. Regarding novel VFs and ARGs, the VFs and ARGs in metagenomic data, and pseudo VFs and ARGs (gene fragments), HyperVR has shown good prediction, outperforming the current state-of-the-art predition tools and best hit approaches in terms of precision and recall. HyperVR is a powerful tool for predicting VFs and ARGs simultaneously by using only gene sequences and without strict cut-off thresholds, hence making prediction straightforward and accurate.
Robust genome editing via modRNA-based Cas9 or base editor in human pluripotent stem cells
Authors: Haideri Tahir , Howells Alessandro , Jiang Yuqian , Yang Jian , Bao Xiaoping , Lian Xiaojun Lance
Published: May 2022

CRISPR systems have revolutionized biomedical research because they offer an unprecedented opportunity to explore the application of genome editing in human pluripotent stem cells (hPSCs). Due to the inherent simplicity of CRISPR systems, requiring a Cas protein and its corresponding single guide RNA (sgRNA), they are more widely adopted and used for diverse biomedical research than their predecessors (zinc finger nucleases and TALENs). However, a bottleneck of applying CRISPR systems in hPSCs is how to deliver CRISPR effectors easily and efficiently into hPSCs. Herein, we developed modified mRNA (modRNA) based CRIPSR systems that utilized Cas9 or base editor (ABE8e) modRNA for genome editing of hPSCs via simple lipid-based transfection. We have achieved 71.09% ± 9.13% and 68.53% ± 3.81% gene knockout (KO) efficiency with Cas9 modRNA and ABE8e modRNA, respectively, which is significantly higher than plasmid-based systems. In summary, we demonstrate that our non-integrating modRNA based CRISPR methods hold great promise as the more efficient and accessible techniques for genome editing of hPSCs.
Bi-phasic patterns of age-related differences in dopamine D1 receptors across the adult lifespan
Authors: Johansson Jarkko , Nordin Kristin , Pedersen Robin , Karalija Nina , Papenberg Goran , Andersson Micael , Korkki Saana M. , Riklund Katrine , Guitart-Masip Marc , Rieckmann Anna , Bäckman Lars , Nyberg Lars , Salami Alireza
Published: May 2022

The dopamine (DA) system, particularly D1-like DA receptors (D1DR), declines across the adult life. The functional consequences of reduced D1DR has been hypothesized to vary across life periods, but the precise timing of these periods is unknown. To examine distinct phases in age-related D1DR reductions, we studied 180 healthy adults (90 females, 20-80 years), who underwent D1DR PET assessment using [11C]SCH23390. A bi-phasic pattern of age-related D1DR differences was revealed, with an inflection point at approximately 40 years of age. Notably, D1DR levels before and after the inflection showed opposing relations to neurocognitive functions, in concordance with distinct consequences of D1DR differences during development and in old age. Furthermore, D1DR reductions in later life were linked to age-related cerebrovascular consequences. These results support a distinction between D1DR reductions in early adulthood from those later in life, and suggest less dramatic and more malleable DA losses in aging than previously suggested.
Reproducible patterns of neural activity without attractors in cortical networks
Authors: Guarino Domenico , Filipchuk Anton , Destexhe Alain
Published: May 2022

Cortical activity often consists of recurring population events of correlated neuronal firing and highly reproducible firing patterns. Because of their resemblance with attractor dynamics, the attractor model prevails today, although it has not been firmly demonstrated. Here, we used a unique dataset, with co-registered two-photon calcium imaging and electron microscopy of the same cortical tissue, to test the central assumption of attractor networks: recurrently active “core” neurons should be strongly interconnected. We report that, contrary to the attractor paradigm, core neurons have fewer weaker connections compared to other neurons. Instead, core neurons funnel the flow of multiple connectivity pathways. Computational models give a mechanistic account of these features showing that distance-dependent connectivity forms converging-diverging motifs and, at their funneling centers, core neurons are found. Thus, reproducible cortical activity and connectivity can be explained without postulating underlying attractor networks but rather by the existence of overlapping information flows.
Induction of Anxiety-Like Phenotypes by Knockout of Cannabinoid Type-1 Receptor in Amygdala of Marmosets
Authors: Zheng Di , Zhu Lin , Li Rui , Shen Chen-Jie , Cai Ruolan , Sun Hao , Wang Xiaohui , Ding Yu , Xu Bin , Jia Guoqiang , Li Xinjian , Gao Lixia , Li Xiao-Ming
Published: May 2022

The amygdala is an important hub for the regulation of emotions, which is crucial for elucidating cellular and molecular mechanisms of many mental diseases. In the central nervous system, the endocannabinoid system plays a key role in the regulation of emotions and mainly functions through the cannabinoid type-1 receptor (CB1R), which is encoded by theCnr1gene. Although CB1R is highly expressed in the amygdala of non-human primates, little is known about its function. Here, we investigated the function of CB1R by knocking out the CB1R in the amygdala of adult marmosets through regional delivery of AAV-SaCas9-gRNA. We found that CB1R knockout in the amygdala of marmosets induced anxiety-like behaviors, including disrupted night sleep, agitated psychomotor activity in new environments, and reduced social desire, but had no effect on hedonic state and fear response. Moreover, CB1R-knockout marmosets exhibited up-regulated plasma cortisol levels, suggesting increased stress. These results showed that knockout of CB1R in the amygdala induced anxiety-like phenotypes in marmosets and shed new light on the mechanisms underlying the regulation of anxiety by CB1R in the amygdala of non-human primates.
Defining the spatial distribution of extracellular adenosine revealed a myeloid-dependent immunosuppressive microenvironment in pancreatic ductal adenocarcinoma
Authors: Graziano Vincenzo , Dannhorn Andreas , Hulme Heather , Williamson Kate , Buckley Hannah , Karim Saadia A , Lee Sheng Y. , Kaistha Brajesh P. , Islam Sabita , Thaventhiran James E. D. , Richards Frances M. , Goodwin Richard , Brais Rebecca , Morton Jennifer P , Dovedi Simon J. , Schuller Alwin G. , Eyles Jim , Jodrell Duncan I.
Published: May 2022

The prognosis for patients with pancreatic ductal adenocarcinoma (PDAC) remains extremely poor. It has been suggested that the adenosine pathway contributes to the ability of PDAC to evade the immune system and its resistance to immunotherapies (Immuno-Oncology Therapy, IOT), by generating extracellular adenosine (eAdo).

Using genetically engineered allograft models of PDAC in syngeneic mice with differential immune infiltration and response to IOT, we showed enrichment of the adenosine pathway in tumour-infiltrating immune cells (in particular, myeloid populations). Using MS-Imaging, we showed that extracellular adenosine distribution is heterogeneous in tumours, with high concentrations in hypoxic margins that surround necrotic areas, associated with a rich myeloid infiltration, demonstrated using Imaging Mass Cytometry (IMC). Pro-tumorigenic M2 macrophages express high levels of the Adora2a receptor; particularly in the IOT resistant model. Blocking thein vivoformation and function of eAdo (Adoi), using a combination of anti-CD73 antibody and an Adora2a inhibitor slowed tumour growth and reduced metastatic burden. In addition, blocking the adenosine pathway improved the efficacy of combinations of cytotoxic agents or immunotherapy. Finally, Adoi remodelled the tumour microenvironment (TME), as evidenced by reduced infiltration of M2 macrophages and Tregs. RNAseq analysis showed that genes related to immune modulation, hypoxia and tumour stroma were downregulated following Adoi and a specific adenosine signature derived from this is associated with a poorer prognosis in patients with PDAC.

The formation of eAdo appears to promote the development of the immunosuppressive TME in PDAC, contributing to its resistance to conventional and novel therapies. Therefore, inhibition of the adenosine pathway may represent a strategy to modulate the stroma and improve therapy response in patients with PDAC.
Unpredictable repeatability in molecular evolution
Authors: Das Suman G , Krug Joachim
Published: May 2022

The extent of parallel evolution at the genotypic level is quantitatively linked to the distribution of beneficial fitness effects (DBFE) of mutations. The standard view, based on light-tailed distributions (i.e. distributions with finite moments), is that the probability of parallel evolution in duplicate populations is inversely proportional to the number of available mutations, and moreover that the DBFE is sufficient to determine the probability when the number of available mutations is large. Here we show that when the DBFE is heavy-tailed, as found in several recent experiments, these expectations are defied. The probability of parallel evolution decays anomalously slowly in the number of mutations or even becomes independent of it, implying higher repeatability of evolution. At the same time, the probability of parallel evolution is non-self-averaging, that is, it does not converge to its mean value even when a large number of mutations are involved. This behavior arises because the evolutionary process is dominated by only a few mutations of high weight. Consequently, the probability varies widely across systems with the same DBFE. Contrary to the standard view, the DBFE is no longer sufficient to determine the extent of parallel evolution, making it much less predictable. We illustrate these ideas theoretically and through analysis of empirical data on antibiotic resistance evolution.
Transitional alveolar epithelial cells and microenvironmental stiffness synergistically drive fibroblast activation in three-dimensional hydrogel lung models
Authors: Caracena Thomas , Blomberg Rachel , Hewawasam Rukshika S. , Riches David W.H. , Magin Chelsea M.
Published: May 2022

Idiopathic pulmonary fibrosis (IPF) is a devastating lung disease that progressively and irreversibly alters the lung parenchyma, eventually leading to respiratory failure. The study of this disease has been historically challenging due to the myriad of complex processes that contribute to fibrogenesis and the inherent difficulty in accurately recreating the human pulmonary environmentin vitro. Here, we describe a poly(ethylene glycol) PEG hydrogel-based three-dimensional model for the co-culture of primary murine pulmonary fibroblasts and alveolar epithelial cells that reproduces the micro-architecture, cell placement, and mechanical properties of healthy and fibrotic lung tissue. Co-cultured cells retained normal levels of viability up to at least three weeks and displayed differentiation patterns observedin vivoduring IPF progression. Interrogation of protein and gene expression within this model showed that myofibroblast activation required both extracellular mechanical cues and the presence of transitional epithelial cells. Differences in gene expression indicated that cellular co-culture induced TGF-β signaling and proliferative gene expression, while microenvironmental stiffness upregulated the expression of genes related to cell-ECM interactions. This biomaterial-based cell culture system serves as a significant step forward in the accurate recapitulation of human lung tissuein vitro, and highlights the need to incorporate multiple factors that work together synergisticallyin vivointo models of lung biology of health and disease.
LKB1 is the gatekeeper of carotid body chemo-sensing and the hypoxic ventilatory response
Authors: MacMillan Sandy , Holmes Andrew P. , Dallas Mark L. , Mahmoud Amira D. , Shipston Michael J. ,   the late Chris Peers, Hardie D. Grahame , Kumar Prem , Evans A. Mark
Published: May 2022

The hypoxic ventilatory response (HVR) is critical to breathing and thus oxygen supply to the body and is primarily mediated by the carotid bodies. Here we reveal that carotid body afferent discharge during hypoxia and hypercapnia is determined by the expression of Liver Kinase B1 (LKB1), the principal kinase that activates the AMP-activated protein kinase (AMPK) during metabolic stresses. Conversely, conditional deletion in catecholaminergic cells of AMPK had no effect on carotid body responses to hypoxia or hypercapnia. By contrast, the HVR was attenuated by LKB1 and AMPK deletion. However, in LKB1 knockouts hypoxia evoked hypoventilation, apnoea and Cheyne-Stokes-like breathing, while only hypoventilation and apnoea were observed after AMPK deletion. We therefore identify LKB1 as an essential regulator of carotid body chemosensing and uncover a divergence in dependency on LKB1 and AMPK between the carotid body on one hand and the HVR on the other.
Drosophila Rif1 is critical for repair following P-element excision and influences pathway choice at double-strand breaks
Authors: Blanch Justin R. , Krishnamurthy Manan , Zuckerman Jacob T. , McVey Mitch
Published: May 2022

Rif1 plays important roles in the repair of DNA double-strand breaks in multiple organisms. In mammals, RIF1 promotes non-homologous end joining and suppresses homologous recombination by interacting with 53BP1 to inhibit resection. In Saccharomyces cerevisiae, Rif1 directly binds DNA to inhibit resection and promote non-homologous end-joining. Yeast Rif1 can also facilitate long-range resection and promote single-strand annealing. Since it is not clear if Rif1 regulates resection-mediated pathway choice in other eukaryotes, we explored the role of Rif1 in double-strand break repair in Drosophila melanogaster. We found that rif1 mutants are not sensitive to ionizing radiation or hydroxyurea, demonstrating that it is not essential for the resolution of DNA damage in Drosophila. However, we show that rif1 null mutants are largely unable to repair a specific type of double-strand break that is induced upon the excision of a P-element transposon. Furthermore, assessment of repair pathway choice at I-SceI-induced breaks revealed Rif1 suppresses homologous recombination and promotes single-strand annealing. Collectively, our findings illustrate Drosophila Rif1 shares functions with both its yeast and mammalian counterparts and serves a unique role in repairing P-element-induced double-strand breaks.
Dissociation of reliability, heritability, and predictivity in coarse- and fine-scale functional connectomes during development
Authors: Busch Erica L. , Rapuano Kristina M. , Anderson Kevin M. , Rosenberg Monica D. , Watts Richard , Casey BJ , Haxby James V. , Feilong Ma
Published: May 2022

The functional connectome supports information transmission through the brain at various spatial scales, from exchange between broad cortical regions to finer–scale, vertex–wise connections that underlie specific information processing mechanisms. In adults, while both the coarse- and fine-scale functional connectomes predict cognition, the fine-scale can predict up to twice the variance as the coarse-scale functional connectome. Yet, past brain-wide association studies, particularly using large developmental samples, focus on the coarse connectome to understand the neural underpinnings of individual differences in cognition. Using a large cohort of children (age 9 – 10 years;n= 1,115 individuals, both sexes, 50% female, including 170 monozygotic and 219 dizygotic twin pairs and 337 unrelated individuals), we examine the reliability, heritability, and behavioral relevance of resting-state functional connectivity computed at different spatial scales. We use connectivity hyperalignment to improve access to reliable fine-scale (vertex–wise) connectivity information and compare the fine-scale connectome with the traditional parcel–wise (coarse scale) functional connectomes. Though individual differences in the fine-scale connectome are more reliable than those in the coarse-scale, they are less heritable. Further, the alignment and scale of connectomes influence their ability to predict behavior, whereby some cognitive traits are equally well predicted by both connectome scales, but other, less heritable cognitive traits are better predicted by the fine-scale connectome. Together, our findings suggest there are dissociable individual differences in information processing represented at different scales of the functional connectome which, in turn, have distinct implications for heritability and cognition.

Significance statement

Years of human magnetic resonance imaging (MRI) research demonstrate that individual variability in resting-state functional connectivity relates to genetics and cognition. However, the various spatial scales where individual differences in connectivity could occur have yet to be considered in childhood brain– behavior association studies. Here, we use novel machine learning approaches to examine the reliability, heritability, and behavioral relevance of different spatial scales of the resting-state functional connectome during childhood. We show that broad features of the connectome are strongly related to heritability, whereas fine details are more reliable and strongly associated with neurocognitive performance. These data indicate that reliable, heritable, and behaviorally–relevant individual differences exist at dissociable scales of the functional connectome.
Acute COG inactivation unveiled its immediate impact on Golgi and illuminated the nature of intra-Golgi recycling vesicles
Authors: Sumya Farhana Taher , Pokrovskaya Irina D. , D’Souza Zinia , Lupashin Vladimir V.
Published: May 2022

Conserved Oligomeric Golgi (COG) complex controls Golgi trafficking and glycosylation, but the precise COG mechanism is unknown. The auxin-inducible acute degradation system was employed to investigate initial defects resulting from COG dysfunction. We found that acute COG inactivation caused a massive accumulation of COG-dependent (CCD) vesicles that carry the bulk of Golgi enzymes and resident proteins. v-SNAREs (GS15, GS28) and v-tethers (giantin, golgin84, and TMF1) were relocalized into CCD vesicles, while t-SNAREs (STX5, YKT6), t-tethers (GM130, p115), and most of Rab proteins remained Golgi-associated. Airyscan microscopy and velocity gradient analysis revealed that different Golgi residents are segregated into different populations of CCD vesicles. Acute COG depletion significantly affected three Golgi-based vesicular coats- COPI, AP1, and GGA, suggesting that COG uniquely orchestrates tethering of multiple types of intra-Golgi CCD vesicles produced by different coat machineries. This study provided the first detailed view of primary cellular defects associated with COG dysfunction in human cells.