bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID-19 Pandemic Severity, Lockdown Regimes, and People’s Mobility: Evidence from 88 Countries
Authors: Rahman Md. Mokhlesur , Thill Jean-Claude , Paul Kamal Chandra
Published: August 2020

This study empirically investigates the complex interplay between the severity of the coronavirus pandemic, mobility changes in retail and recreation, transit stations, workplaces, and residential areas, and lockdown measures in 88 countries of the word. To conduct the study, data on mobility patterns, socioeconomic and demographic characteristics of people, lockdown measures, and coronavirus pandemic were collected from multiple sources (e.g., Google, UNDP, UN, BBC, Oxford University, Worldometer). A Structural Equation Modeling (SEM) technique is used to investigate the direct and indirect effects of independent variables on dependent variables considering the intervening effects of mediators. Results show that lockdown measures have significant effects to encourage people to maintain social distancing. However, pandemic severity and socioeconomic and institutional factors have limited effects to sustain social distancing practice. The results also explain that socioeconomic and institutional factors of urbanity and modernity have significant effects on pandemic severity. Countries with a higher number of elderly people, employment in the service sector, and higher globalization trend are the worst victims of the coronavirus pandemic (e.g., USA, UK, Italy, and Spain). Social distancing measures are reasonably effective at tempering the severity of the pandemic.
EVALUATION OF THE DURABILITY OF LONG-LASTING INSECTICIDAL NETS IN GUATEMALA
Authors: Castellanos María Eugenia , Rodas Soledad , Juarez Jose Guillermo , Lol Juan Carlos , Chanquin Sayra , Morales Zoraida , Vizcaino Lucrecia , Smith Stephen C. , Eng Jodi Vanden , Woldu Henok G. , Lenhart Audrey , Padilla Norma
Published: August 2020

Background

Insecticide-treated bednets (ITNs) are widely used for the prevention and control of malaria. In Guatemala, since 2006, ITNs have been distributed free of charge in the highest risk malaria-endemic areas and constitute one of the primary vector control measures in the country. Despite relying on ITNs for almost 15 years, there is a lack of data to inform the timely replacement of ITNs whose effectiveness becomes diminished by routine use.

Methods

We assessed the survivorship, physical integrity, insecticide content and bio-efficacy of ITNs through cross-sectional surveys conducted at 18, 24 and 32 months after a 2012 distribution of PermaNet® 2.0 in a malaria focus in Guatemala. A total of 988 ITNs were analyzed (290 at 18 months, 349 at 24 months and 349 at 32 months).

Results

The functional survivorship of bednets decreased over time, from 92% at 18 months, to 81% at 24 months and 69% at 32 months. Independent of the time of the survey, less than 80% of the bednets that were still present in the household were reported to have been used the night before. Most of the bednets had been washed at least once (88% at 18 months, 92% at 24 months and 96% at 32 months). The proportion of bednets categorized as “in good condition” per WHO guidelines of the total hole surface area, diminished from 77% at 18 months to 58% at 32 months. The portion of ITNs with deltamethrin concentration less than 10mg/m2 increased over time (14% at 18 months, 23% at 24 months, and 35% at 32 months). Among the bednets for which bioassays were conducted, the percentage that met WHO criteria for efficacy dropped from 90% at 18 months to 52% at 32 months.

Conclusion

While our assessment demonstrated that nets were in relatively good physical condition over time, the combination of declining bio-efficacy over time and low use rates limited the overall effectiveness of the LLINs. Efforts to encourage the community to retain, use, and properly care for the LLINs may improve their impact. Durability assessments should be included in future campaigns.
Central nervous system immune response in postinfectious hydrocephalus
Authors: Isaacs Albert M. , Morton Sarah U. , Movassagh Mercedeh , Zhang Qiang , Hehnly Christine , Zhang Lijun , Morales Diego M. , Sinnar Shamim A. , Ericson Jessica E , Kabachelor Edith , Ssenyonga Peter , Onen Justin , Mulondo Ronnie , Hornig Mady , Warf Benjamin C. , Broach James R. , Townsend R Reid , Limbrick David D. , Paulson Joseph N. , Schiff Steven J.
Published: August 2020

Inflammation following neonatal infection is a dominant cause of childhood hydrocephalus in the developing world. Understanding this complex inflammatory response is critical for the development of preventive therapies. In 100 African hydrocephalic infants ≤3 months of age, with and without a history of infection, we elucidated the biological pathways that account for this inflammatory response. We integrated proteomics and RNA sequencing in cerebrospinal fluid, identifying gene pathways involving neutrophil, interleukin (4, 12, and 13) and interferon activity associated with this condition. These findings are required to develop strategies to reduce the risk of hydrocephalus during treatment of infection.
Comparison of sixteen serological SARS-CoV-2 immunoassays in sixteen clinical laboratories
Authors: Harritshøj Lene H. , Gybel-Brask Mikkel , Afzal Shoaib , Kamstrup Pia R. , Jørgensen Charlotte S. , Thomsen Marianne Kragh , Hilsted Linda , Friis-Hansen Lennart , Szecsi Pal B. , Pedersen Lise , Nielsen Lene , Hansen Cecilie B. , Garred Peter , Korsholm Trine-Line , Mikkelsen Susan , Nielsen Kirstine O. , Møller Bjarne K. , Hansen Anne T. , Iversen Kasper K. , Nielsen Pernille B. , Hasselbalch Rasmus B. , Fogh Kamille , Norsk Jakob B. , Kristensen Jonas Henrik , Schønning Kristian , Kirkby Nikolai S. , Nielsen Alex C. Y. , Landsy Lone H. , Loftager Mette , Holm Dorte K. , Nilsson Anna C. , Sækmose Susanne G. , Grum-Schwensen Birgitte , Aagaard Bitten , Jensen Thøger G. , Nielsen Dorte M. , Ullum Henrik , Dessau Ram B.C.
Published: August 2020

Serological SARS-CoV-2 assays are needed to support clinical diagnosis and epidemiological investigations. Recently, assays for the large-volume detection of total antibodies (Ab) and immunoglobulin (Ig) G and M against SARS-CoV-2 antigens have been developed, but there are limited data on the diagnostic accuracy of these assays. This study was organized as a Danish national collaboration and included fifteencommercial and one in-house anti-SARS-CoV-2 assays in sixteen laboratories. Sensitivity was evaluated using 150 serum samples from individuals diagnosed with asymptomatic,mild or moderate nonhospitalized (n=129) or hospitalized (n=31) COVID-19, confirmed bynucleic acid amplification tests, collected 13-73 days from symptom onset. Specificity and cross-reactivity were evaluated in samples collected prior to the SARS-CoV-2 epidemic from > 586 blood donors and patients with autoimmune diseases or CMV or EBV infections. Predefined specificity criteria of ≥ 99% were met by all total-Ab and IgG assays except one (Diasorin/LiaisonXL-IgG 97.2%). The sensitivities in descending order were: Wantai/ELISA total-Ab (96.7%), CUH/NOVO in-house ELISA total-Ab (96.0%), Ortho/Vitros total-Ab (95.3%), YHLO/iFlash-IgG (94.0%), Ortho/Vitros-IgG (93.3%), Siemens/Atellica total-Ab (93.2%), Roche-Elecsys total-Ab (92.7%), Abbott-Architect-IgG (90.0%), Abbott/Alinity-IgG (median 88.0%), Diasorin/LiaisonXL-IgG (84.6%),Siemens/Vista total-Ab (81.0%), Euroimmun/ELISA-IgG (78.0%), and Snibe/Maglumi-IgG (median 78.0%). The IgM results were variable, but one assay (Wantai/ELISA-IgM) hadboth high sensitivity (82.7%) and specificity (99%). The rate of seropositivity increased with time from symptom onset and symptom severity. In conclusion, predefined sensitivity and specificity acceptance criteria of 90%/99%, respectively, for diagnostic use were met in five of six total-Ab and three of seven IgG assays.
Covid-19 mortality rates in Northamptonshire UK: initial sub-regional comparisons and provisional SEIR model of disease spread
Authors: Petford Nick , Campbell Jackie
Published: August 2020

Objectives

We analysed mortality rates in a nonmetropolitan UK subregion (Northamptonshire) to understand SARSCoV2 disease fatalities at sub 1,000,000 population levels. A numerical (SEIR) model was then developed to predict the spread of Covid19 in Northamptonshire.

Methods

A combined approach using statistically-weighted data to fit the start of the epidemic to the mortality record. Parameter estimates were then derived for the transmission rate and basic reproduction number.

Results

Age standardised mortality rates are highest in Northampton (urban) and lowest in semi-rural districts. Northamptonshire has a statistically higher Covid-19 mortality rate than for the East Midlands and England as a whole. Model outputs suggest the number of infected individuals exceed official estimates, meaning less than 40% of the population may require immunisation.

Conclusions

Combining published (sub-regional) mortality rate data with deterministic models on disease spread has the potential to help public health practitioners develop bespoke mitigations, guided by local population demographics.
The Ontario Neurodegenerative Disease Research Initiative
Authors: Sunderland Kelly M. , Beaton Derek , Arnott Stephen R. , Kleinstiver Peter , Kwan Donna , Lawrence-Dewar Jane M. , Ramirez Joel , Tan Brian , Bartha Robert , Black Sandra E. , Borrie Michael , Brien Donald , Casaubon Leanne K. , Coe Brian C. , Cornish Benjamin , Dilliott Allison A. , Dowlatshahi Dar , Finger Elizabeth , Fischer Corinne , Frank Andrew , Fraser Julia , Freedman Morris , Greenberg Barry , Grimes David A. , Hassan Ayman , Hatch Wendy , Hegele Robert A. , Hudson Christopher , Jog Mandar , Kumar Sanjeev , Lang Anthony , Levine Brian , Lou Wendy , Mandzia Jennifer , Marras Connie , McIlroy William , Montero-Odasso Manuel , Munoz David G. , Munoz Douglas P. , Orange Joseph B. , Park David S. , Pasternak Stephen H. , Faria Frederico Pieruccini- , Rajji Tarek K. , Roberts Angela C. , Robinson John F. , Rogaeva Ekaterina , Sahlas Demetrios J. , Saposnik Gustavo , Scott Christopher J.M. , Seitz Dallas , Shoesmith Christen , Steeves Thomas D.L. , Strong Michael J. , Strother Stephen C. , Swartz Richard H. , Symons Sean , Tang-Wai David F. , Tartaglia Maria Carmela , Troyer Angela K. , Turnbull John , Zinman Lorne , McLaughlin Paula M. , Masellis Mario , Binns Malcolm A.
Published: August 2020

Objective

In individuals over the age of 65, concomitant neurodegenerative pathologies contribute to cognitive and/or motor decline and can be aggravated by cerebrovascular disease, but our understanding of how these pathologies synergize to produce the decline represents an important knowledge gap. The Ontario Neurodegenerative Disease Research Initiative (ONDRI), a multi-site, longitudinal, observational cohort study, recruited participants across multiple prevalent neurodegenerative diseases and cerebrovascular disease, collecting a wide array of data and thus allowing for deep investigation into common and unique phenotypes. This paper describes baseline features of the ONDRI cohort, understanding of which is essential when conducting analyses or interpreting results.

Methods

Five disease cohorts were recruited: Alzheimer’s disease/amnestic mild cognitive impairment (AD/MCI), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Parkinson’s disease (PD), and cerebrovascular disease (CVD). Assessment platforms included clinical, neuropsychology, eye tracking, gait and balance, neuroimaging, retinal imaging, genomics, and pathology. We describe recruitment, data collection, and data curation protocols, and provide a summary of ONDRI baseline characteristics.

Results

520 participants were enrolled. Most participants were in the early stages of disease progression. Participants had a median age of 69 years, a median Montreal Cognitive Assessment score of 25, a median percent of independence of 100 for basic activities of daily living, and a median of 93 for instrumental activities. Variation between disease cohorts existed for age, level of cognition, and geographic location.

Conclusion

ONDRI data will enable exploration into unique and shared pathological mechanisms contributing to cognitive and motor decline across the spectrum of neurodegenerative diseases.
Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score
Authors: Knight Stephen R , Ho Antonia , Pius Riinu , Buchan Iain , Carson Gail , Drake Thomas M , Dunning Jake , Fairfield Cameron J , Gamble Carrol , Green Christopher A , Gupta Rishi , Halpin Sophie , Hardwick Hayley E , Holden Karl A , Horby Peter W , Jackson Clare , Mclean Kenneth A , Merson Laura , Nguyen-Van-Tam Jonathan S , Norman Lisa , Noursadeghi Mahdad , Olliaro Piero L , Pritchard Mark G , Russell Clark D , Shaw Catherine A , Sheikh Aziz , Solomon Tom , Sudlow Cathie , Swann Olivia V , Turtle Lance CW , Openshaw Peter JM , Baillie J Kenneth , Semple Malcolm G , Docherty Annemarie B , Harrison Ewen M
Published: August 2020

Objectives

To develop and validate a pragmatic risk score to predict mortality for patients admitted to hospital with covid-19.

Design

Prospective observational cohort study: ISARIC WHO CCP-UK study (ISARIC Coronavirus Clinical Characterisation Consortium [4C]). Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited between 21 May and 29 June 2020.

Setting

260 hospitals across England, Scotland, and Wales.

Participants

Adult patients (≥18 years) admitted to hospital with covid-19 admitted at least four weeks before final data extraction.

Main outcome measures

In-hospital mortality.

Results

There were 34 692 patients included in the derivation dataset (mortality rate 31.7%) and 22 454 in the validation dataset (mortality 31.5%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea, and C-reactive protein (score range 0-21 points). The 4C risk stratification score demonstrated high discrimination for mortality (derivation cohort: AUROC 0.79; 95% CI 0.78 − 0.79; validation cohort 0.78, 0.77-0.79) with excellent calibration (slope = 1.0). Patients with a score ≥15 (n = 2310, 17.4%) had a 67% mortality (i.e., positive predictive value 67%) compared with 1.0% mortality for those with a score ≤3 (n = 918, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (AUROC range 0.60-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).

Conclusions

We have developed and validated an easy-to-use risk stratification score based on commonly available parameters at hospital presentation. This outperformed existing scores, demonstrated utility to directly inform clinical decision making, and can be used to stratify inpatients with covid-19 into different management groups. The 4C Mortality Score may help clinicians identify patients with covid-19 at high risk of dying during current and subsequent waves of the pandemic.

Study registration

ISRCTN66726260
The integrated approach of learning tuberculosis transmission within and outside households via random directed graph models
Authors: Li Tenglong , Jones-L□pez Edward C. , White Laura F.
Published: August 2020

Household contact studies are frequently used in tuberculosis transmission research, and models based on them often focus on transmission within the household. This contradicts recent research which suggests the transmission may be more likely to happen outside the household than within the household in high burden settings where these studies are frequently conducted. Consequently, most models would lead to biased estimates and misleading public health interventions. There is a strong need for developing models that allow concurrent estimation of household and extra-household transmission. In this study, we develop a random directed graph model for tuberculosis transmission, which permits users to concurrently build models for both household and extra-household transmission. Furthermore, our model can estimate the relative frequency of household transmission versus extra-household transmission and consistently produce unbiased estimates for risk factors, regardless of whether community controls are available. We illustrate our approach with a household contact study conducted in Vitória, Brazil, and our results indicate that extra-household transmission can account for 63% to 98% of M. tuberculosis infections detected during such a study.
Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity
Authors: Luo Yiqi Ruben , Chakraborty Indrani , Yun Cassandra , Wu Alan H.B. , Lynch Kara L.
Published: August 2020

The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. The IgG avidity assay used a novel label-free immunoassay technology. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases.
Data-driven modeling and forecasting of COVID-19 outbreak for public policy making
Authors: Hasan A. , Putri E.R.M. , Susanto H. , Nuraini N.
Published: August 2020

This paper presents a data-driven approach for COVID-19 outbreak modeling and forecasting, which can be used by public policy and decision makers to control the outbreak through Non-Pharmaceutical Interventions (NPI). First, we apply an extended Kalman filter (EKF) to a discrete-time stochastic augmented compartmental model to estimate the time-varying effective reproduction number ℛt. We use daily confirmed cases, active cases, recovered cases, deceased cases, Case-Fatality-Rate (CFR), and infectious time as inputs for the model. Furthermore, we define a Transmission Index (TI) as a ratio between the instantaneous and the maximum value of the effective reproduction number. The value of TI shows the disease transmission in a contact between a susceptible and an infectious individual due to current measures such as physical distancing and lock-down relative to a normal condition. Based on the value of TI, we forecast different scenarios to see the effect of relaxing and tightening public measures. Case studies in three countries are provided to show the practicability of our approach.
Visuospatial attention revamps cortical processing of sound: restrict stimulus uncertainty
Authors: Cervantes Constantino F. , Sánchez-Costa T. , Cipriani G. A. , Carboni A.
Published: August 2020

Selective attentional biases arising from one sensory modality may manifest in another. The effects of visuospatial attention, often considered a foundation for visual object perception, are unclear in the auditory domain during audiovisual (AV) scene processing. This study investigates temporal and spatial factors that facilitate such cross-modal bias transfer at the neural level. Auditory encoding of random tone pips in AV scenes was investigated via a temporal response function model (TRF) of the participants’ electroencephalogram (N=30). The spatially uninformative pips were associated with spatially distributed visual contrast reversals (‘flips’) through asynchronous, probabilistic AV temporal onset distributions. Participants deployed visuospatial selection on these AV stimuli to perform a task. A late (~300 ms) cross-modal transfer of the unimodal attentional bias was found on the neural representation of pips. Transfer depended on the selected visual input being (i) presented during or shortly after a related sound in a relatively limited temporal window (<165 ms); and (ii) positioned across limited (1:4) visual foreground to background ratios. In addition, the magnitude of attentional enhancement was proportional to the proximity of flips to the foreground area. The results indicate that ongoing neural representations of sounds can incorporate relevant visuospatial attributes for auditory stream segregation.
Hybrid capture-based sequencing enables unbiased recovery of SAR-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants
Authors: Xu Yi , Kang Lu , Shen Zijie , Li Xufang , Wu Weili , Ma Wentai , Fang Chunxiao , Yang Fengxia , Jiang Xuan , Gong Sitang , Zhang Li , Li Mingkun
Published: August 2020

Background

In response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples.

Methods

Eighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization.

Results

By examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period.

Conclusions

The hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.
Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy
Authors: Barone Sierra M. , Paul Alberta G.A. , Muehling Lyndsey M. , Lannigan Joanne A. , Kwok William W. , Turner Ronald B. , Woodfolk Judith A. , Irish Jonathan M.
Published: August 2020

For an emerging disease like COVID-19, systems immunology tools may quickly identify and quantitatively characterize cells associated with disease progression or clinical response. With repeated sampling, immune monitoring creates a real-time portrait of the cells reacting to a novel virus before disease specific knowledge and tools are established. However, single cell analysis tools can struggle to reveal rare cells that are under 0.1% of the population. Here, the machine learning workflow Tracking Responders Expanding (T-REX) was created to identify changes in both very rare and common cells in diverse human immune monitoring settings. T-REX identified cells that were highly similar in phenotype and localized to hotspots of significant change during rhinovirus and SARS-CoV-2 infections. Specialized reagents used to detect the rhinovirus-specific CD4+cells, MHCII tetramers, were not used during unsupervised analysis and instead ‘left out’ to serve as a test of whether T-REX identified biologically significant cells. In the rhinovirus challenge study, T-REX identified virus-specific CD4+T cells based on these cells being a distinct phenotype that expanded by ≥95% following infection. T-REX successfully identified hotspots containing virus-specific T cells using pairs of samples comparing Day 7 of infection to samples taken either prior to infection (Day 0) or after clearing the infection (Day 28). Mapping pairwise comparisons in samples according to both the direction and degree of change provided a framework to compare systems level immune changes during infectious disease or therapy response. This revealed that the magnitude and direction of systemic immune change in some COVID-19 patients was comparable to that of blast crisis acute myeloid leukemia patients undergoing induction chemotherapy and characterized the identity of the immune cells that changed the most. Other COVID-19 patients instead matched an immune trajectory like that of individuals with rhinovirus infection or melanoma patients receiving checkpoint inhibitor therapy. T-REX analysis of paired blood samples provides an approach to rapidly identify and characterize mechanistically significant cells and to place emerging diseases into a systems immunology context.
Specific mutations in genes responsible for Alzheimer and for Duchenne Muscular Dystrophy introduced by Base editing and PRIME editing
Authors: Rousseau Joël , Mbakam Cédric Happi , Guyon Antoine , Tremblay Guillaume , Begin Francis Gabriel , Tremblay Jacques P.
Published: August 2020

Base editing technique and PRIME editing techniques derived from the CRISPR/Cas9 discovery permit to modify selected nucleotides. We initially used the base editing technique to introduce in theAPPgene the A673T mutation, which prevents the development of Alzheimer’s disease. Although the desired cytidine to thymidine mutation was inserted in up to 17% of theAPPgene in HEK393T, there were also modifications of up to 20% of other nearby cytidines. More specific mutations of theAPPgene were obtained with the PRIME editing technique. However, the best percentage of mutations was only 5.8%. The efficiency of the PRIME editing treatment was initially tested on theEMX1gene. A single treatment produced the desired modification in 36% of theEMX1gene. Three consecutive treatments increased the percentage of mutations to 50%. The PRIME editing technique was also used to insert specific point mutations in exons 9 and 35 of theDMDgene coding for the dystrophin gene and which is mutated in Duchenne Muscular Dystrophy (DMD). Up to 10% desired mutations of theDMDgene were obtained. Three repeated treatments increased the percentage of specific mutations to 16%. Given that there are thousands of nuclei inside a human muscle fiber and that the dystrophin nuclear domain is about 500 μm, this level of modifications would be sufficient to produce a phenotype improvement in DMD patients.
Developmental Incongruity as a Dynamical Representation of Heterochrony
Authors: Alicea Bradly
Published: August 2020

The theory of heterochrony provides us with a generalized quantitative perspective on the dynamics of developmental trajectories. While useful, these linear developmental trajectories merely characterize changes in the speed and extent of growth in developmental time. One open problem in the literature involves how to characterize developmental trajectories for rare and incongruous modes of development. By combining nonlinear mathematical representations of development with models of gene expression networks (GRNs), the dynamics of growth given the plasticity and complexity of developmental timing are revealed. The approach presented here characterizes heterochrony as a dynamical system, while also proposing a computational motif in GRNs called triangular state machines (TSMs). TSMs enable local computation of phenotypic enhancement by producing nonlinear and potentially unexpected outputs. With a focus on developmental timing and a focus on sequential patterns of growth, formal techniques are developed to characterize delays and bifurcations in the developmental trajectory. More generally, growth is demonstrated using two conceptual models: a Galton board representing axial symmetry and a radial tree depicting differential growth. These techniques take into consideration the existence of multiple developmental genotypes operating in parallel, which ultimately characterize the exquisite phenotypic diversity observed in animal development.
The cooperative assembly of shelterin bridge provides a kinetic gateway that controls telomere length homeostasis
Authors: Liu Jinqiang , Hu Xichan , Bao Kehan , Kim Jin-Kwang , Jia Songtao , Qiao Feng
Published: August 2020

Shelterin is a six-proteins complex that coats chromosome ends to ensure their proper protection and maintenance. Similar to the human shelterin, fission yeast shelterin is composed of telomeric double- and single-stranded DNA-binding proteins, Taz1 and Pot1, respectively, bridged by Rap1, Poz1, and Tpz1. The assembly of the proteinaceous Tpz1-Poz1-Rap1 complex occurs cooperatively and disruption of this shelterin bridge leads to unregulated telomere elongation. However, how this biophysical property of bridge assembly is integrated into shelterin function is not known. Here, utilizing synthetic bridges with a range of binding properties, we find that synthetic shelterin bridge lacking cooperativity requires a linker pair that matches the native bridge in complex lifespan but has dramatically higher affinity. We find that cooperative assembly confers kinetic properties on the shelterin bridge allowing disassembly to function as a molecular timer, regulating the duration of the telomere open state, and consequently telomere lengthening to achieve a defined species-specific length range.
Minicells as a potential chassis for engineering lineage-agnostic organisms
Authors: Wei Eric , Jackson-Smith Anton , Endy Drew
Published: August 2020

Background

Genomes encode for organisms and thus genome synthesis implies the possibility of organismal synthesis, including the synthesis of organisms without constraint to lineage. Current genome-scale engineering projects are focused on minimization, refactoring, or recoding within the context of existing natural lineages. Minicells arise naturally as anucleate cells that are devoid of heritable genetic material but are capable of gene expression. Thus, minicells may serve as a useful starting point for developing lineage-agnostic organisms encoded by newly-designed synthetic genomes. However, the composition and expression capacity of minicells is fixed at the time of their formation. The possibility of reestablishing cellular growth and division starting from minicells and entirely heterologous synthetic genomes is unknown.

Results

We observed expression and segregation of functional proteins among mixed populations of reproducing cells and so-derived anucleate minicells via fluorescence microscopy. By adapting and integrating established methods of preparation and purification we were able to isolate minicells from a growing population of progenitor cells with a purity of at least 500 minicells per progenitor. We then used heterologous expression of plasmid-encoded green fluorescent protein to estimate the absolute expression capacity of minicells. We found that minicells can support the formation of 4.9 ± 4.6 × 108peptide bonds prior to exhausting their initial intrinsic expression capacity.

Conclusions

Minicells can be produced in large numbers with high purity and can also harbor and express engineered plasmids. The observed variation in minicell gene expression capacity suggests that about 13% of gene-expressing minicells can support the formation of more than one-billion peptide bonds, an amount sufficient to replicate known prokaryotic proteomes. Stated differently, while most minicells would require a sophisticated genetic ‘boot’ program to first increase minicell-specific expression capacity sufficient to instantiate newly reproducing lineages, a subset of minicells may be able to directly support whole genome, lineage-agnostic organism engineering.
Antibody:CD47 ratio regulates macrophage phagocytosis through competitive receptor phosphorylation
Authors: Suter Emily C. , Schmid Eva M. , Voets Erik , Francica Brian , Fletcher Daniel A.
Published: August 2020

Cancer immunotherapies often modulate macrophage effector function by introducing either targeting antibodies that activate Fc gamma receptors or blocking antibodies that disrupt inhibitory SIRPα-CD47 engagement. Yet how these competing signals are integrated is poorly understood mechanistically, raising questions about how to effectively titrate immune responses. Here we find that macrophage phagocytic decisions are regulated by the ratio of activating ligand to inhibitory ligand on targets over a broad range of absolute molecular densities. Using endogenous as well as chimeric receptors, we show that activating:inhibitory ligand ratios of at least 10:1 are required to promote phagocytosis of model antibody-opsonized CD47-inhibited targets and that lowering this ratio reduces FcγR phosphorylation due to inhibitory phosphatases recruited to CD47-bound SIRPα. We demonstrate that ratiometric signaling is critical for phagocytosis of tumor cells and can be modified by blocking SIRPαin vitro, indicating that balancing targeting and blocking antibodies may be important for controlling macrophage phagocytosis in cancer immunotherapy.
Predator: A novel method for targeted protein degradation
Authors: Liu Chuanyang , Kuang Jingyu , Qiu Xinyuan , Min Lu , Li Wenying , Ma Jiaxin , Zhu Lingyun
Published: August 2020

Protein expression and degradation are fundamental to cell function and physiological status of organisms. Interfering with protein expression not only provides powerful strategies to analyze the function of proteins but also inspires effective treatment methods for diseases caused by protein dysfunction. Recently, harnessing the power of the ubiquitin-proteasome system for targeted protein degradation (TPD) has become the focus of researches. Over the past two decades, TPD technologies, such as E3 ligase modification, PROTACs, and the Trim-Away method, have successfully re-oriented the ubiquitin-proteasome pathway and thus degraded many pathogenic proteins and even "undruggable" targets. However, A low-cost, convenient, and modularized TPD method is currently not available. Herein, we proposed a synthetic biology TPD method, termed Predator, by integrating the classic function of E3 ligase Trim21 and the expression of a bifunctional fusion protein that links Trim21 and the target protein, which leads to the formation of a ternary complex inside mammalian cells and therefore induce the ubiquitination and subsequent proteasome-dependent degradation of the target protein. We first proved this concept by using nanobody and scFv as the targeting module for the Predator system to degrade free GFP and membrane protein ErbB3, respectively. Then, we give an example of how the engineered Predator system can be developed towards biomedical solutions in the context of diabetes mellitus. Ligands-receptor interaction and adenovirus-mediated gene delivery were introduced to the Predator system, and we found this bifunctional fusion protein, in which glucagon was selected to function as the targeting module, downregulated the endogenous glucagon receptor (GCGR) and attenuated glucagon-stimulated glucose production in primary hepatocytes. Although preliminarily, our results showed that this Predator system is a highly modularized and convenient TPD method with good potential for both fundamental researches and clinical usage.

Graphic abstract
Myocardial matrix material supports a proliferative microenvironment for cardiomyocytes
Authors: Wang Raymond M. , Cattaneo Paola , Camboa Nuno , Braden Rebecca , Luo Colin , Evans Sylvia , Christman Karen L.
Published: August 2020

Novel therapeutics have sought to stimulate the endogenous repair mechanisms in the mammalian myocardium as the native regenerative potential of the adult cardiac tissue is limited. In particular, a myocardial matrix derived injectable hydrogel has shown efficacy and safety in various animal myocardial infarction (MI) including evidence of increased myocardium. In this study, investigation on the properties of this myocardial matrix material demonstrated its native capability as an effective reactive oxygen species (ROS) scavenger that can protect against oxidative stress and maintain cardiomyocyte proliferationin vitro. In vivoassessment of of myocardial matrix hydrogel treatment post-MI demonstrated increased thymidine analog uptake in cardiomyocytes compared to saline controls along with co-staining with cell cycle progression marker, phospho-histone H3. Overall, this study provides further evidence that properties of the myocardial matrix hydrogel promote an environment supportive of cardiomyocytes undergoing cell cycle progression.
P-bodies are sites of rapid RNA decay during the neural crest epithelial—mesenchymal transition
Authors: Hutchins Erica J. , Piacentino Michael L. , Bronner Marianne E.
Published: August 2020

The epithelial—mesenchymal transition (EMT) drives cellular movements during development to create specialized tissues and structures in metazoans, using mechanisms often coopted during metastasis. Neural crest cells are a multipotent stem cell population that undergo a developmentally regulated EMT and are prone to metastasis in the adult, providing an excellent model to study cell state changes and mechanisms underlying EMT. A hallmark of neural crest EMT during avian development is temporally restricted expression followed by rapid down-regulation of the Wnt antagonistDraxin. Using live RNA imaging, here we demonstrate that rapid clearance ofDraxintranscripts is mediated post-transcriptionally via localization to processing bodies (P-bodies), small cytoplasmic granules which are established sites of RNA processing. Contrasting with recent work in immortalized cell lines suggesting that P-bodies are sites of storage rather than degradation, we show that targeted decay ofDraxinoccurs within P-bodies during neural crest migration. Furthermore, P-body disruption viaDDX6knockdown inhibits not only endogenousDraxindown-regulation but also neural crest EMTin vivo. Together, our data highlight a novel and important role for P-bodies in an intact organismal context—controlling a developmental EMT program via post-transcriptional target degradation.
Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogen
Authors: Liu Hongwei , Li Jiayu , Cavalhais Lilia C. , Percy Cassandra , Verma Jay Prakash , Schenk Peer M. , Singh Brajesh
Published: August 2020

Emerging experimental framework suggests that plants under biotic stress may actively seek help from soil microbes, but empirical evidence underlying such a ‘cry for help’ strategy is limited.

We used integrated microbial community profiling, pathogen and plant transcriptive gene quantification and culture-based methods to systematically investigate a three-way interaction between the wheat plant, wheat-associated microbiomes andFusarium pseudograminearum(Fp).

A clear enrichment of a dominant bacterium,Stenotrophomonas rhizophila(SR80), was observed in both the rhizosphere and root endosphere ofFp-infected wheat. SR80 reached 3.7×107cells g-1in the rhizosphere and accounted for up to 11.4% of the microbes in the root endosphere. Its abundance had a positive linear correlation with the pathogen load at base stems and expression of multiple defense genes in top leaves. Upon re-introduction in soils, SR80 enhanced plant growth, both the below- and above-ground, and induced strong disease resistance by priming plant defense in the aboveground plant parts, but only when the pathogen was present

Together, the bacterium SR80 seems to have acted as an early warning system for plant defense. This work provides novel evidence for the potential protection of plants against pathogens by an enriched beneficial microbe via modulation of the plant immune system.
Bone marrow adipogenic lineage precursors (MALPs) promote osteoclastogenesis in bone remodeling and pathologic bone loss
Authors: Yu Wei , Zhong Leilei , Yao Lutian , Wei Yulong , Gui Tao , Li Ziqing , Kim Hyunsoo , Dyment Nathaniel , Liu Xiaowei S. , Yang Shuying , Choi Yongwon , Ahn Jaimo , Qin Ling
Published: August 2020

Bone is maintained by coupled activities of bone-forming osteoblasts/osteocytes and bone-resorbing osteoclasts and an alternation of this relationship can lead to pathologic bone loss such as in osteoporosis. It is well known that osteogenic cells support osteoclastogenesis via synthesizing RANKL. Interestingly, our recently identified bone marrow mesenchymal cell population—marrow adipogenic lineage precursors (MALPs) that form a multi-dimensional cell network in bone—was computationally demonstrated to be the most interactive with monocyte-macrophage lineage cells through highly and specifically expressing several osteoclast regulatory factors, including RANKL. Using an adipocyte-specificAdipoq-Creto label MALPs, we demonstrated that mice with RANKL deficiency in MALPs have a drastic increase of trabecular bone mass in long bones and vertebrae starting from 1 month of age but that their cortical bone is normal. This phenotype was accompanied by diminished osteoclast number and attenuated bone formation at the trabecular bone surface. Reduced RANKL signaling in calvarial MALPs also abolished osteolytic lesions after lipopolysaccharide (LPS) injections. Furthermore, in ovariectomized mice, elevated bone resorption was partially attenuated by RANKL deficiency in MALPs. In summary, our studies identified MALPs as a critical player in controlling bone remodeling during normal bone metabolism and pathological bone loss in a RANKL-dependent fashion.
Multifaceted functions of Rab23 on primary cilium and Hedgehog signaling-mediated granule cell proliferation
Authors: Hor CHH , Leong WY , Goh ELK
Published: August 2020

Sonic Hedgehog (Shh) signaling from the primary cilium drives cerebellar granule cell precursor (GCP) proliferation. Mutations of hedgehog (Hh) pathway repressors could cause medulloblastoma, the most prevalent and malignant childhood brain tumor that arises from aberrant GCP proliferation. We demonstrate that brain-specific knockout of a Shh pathway repressorRab23in mice caused mis-patterning of cerebellar folia and elevated GCP proliferation during early development, but with no prevalent occurrence of medulloblastoma at adult stage. Strikingly,Rab23-depleted GCPs exhibited up-regulated basal level of Shh pathway activities despite reduced ciliation, and were desensitized against stimulations by Shh and Smoothened (Smo) agonist in primary GCP culture. These results illustrate dual functions of Rab23 in repressing the basal level of Shh signaling, while facilitating Shh signal transduction via Shh/Smo on primary cilium. Collectively, our findings unravel instrumental roles ofRab23in GCP proliferation and ciliogenesis.Rab23’spotentiation of Shh signaling pathway through the primary cilium and Smo, suggests a potential new therapeutic for Smo/primary cilium-driven medulloblastoma.

Author Summary

C.H.H conceived, designed, lead, and performed allin vitroandin vivoexperiments, analyzed data and wrote the manuscript. W.Y performed QPCR experiments and primary GCP cultures and analyzed data. E.L.G conceived and directed the study.
Bridging the Gap: From Neuroanatomical Knowledge to Tractography of Brain Pathways
Authors: Gallardo Guillermo , Wassermann Demian , Anwander Alfred
Published: August 2020

Despite recent advances in tractography, the gap remains wide between the descriptions of white-matter pathways in the literature and the methods to reconstruct and study them from dMRI images. Here, we tackle this challenge by proposing a language to define white matter tracts, namely WMQLT, and a tool to automatically reconstruct pathways from their WMQLTqueries. Our method is performant, flexible enough to allow defining tracts using multiple modalities, and allows to extend ROI-based reconstruction methods. Leveraging our language, we define 19 major brain tracts, alongside their subdivisions, and reconstruct them in a large population. We show that the shape of the reconstructed pathways, as well as their connectivity and lateralizations are in accordance with the current neuroanatomical literature. Finally, we showcase our technique in two scenarios: computing the functional subdivisions of a tract, and assessing the role of handedness and gender in the lateralization of language-related tracts.
Different dimensions of robustness - noise, topology and rates - are nearly independent in chemical switches
Authors: Moza Sahil , Bhalla Upinder S.
Published: August 2020

Life prospers despite adverse conditions in many unpredictable dimensions. This requires that cellular processes work reliably, that is they are robust against many kinds of perturbations. For example, a cellular decision to differentiate should be stable despite changes in metabolic conditions and stochasticity due to thermal noise. For evolutionary stability, the same differentiation switch should function despite mutations or the evolution of further regulatory inputs. We asked how cellular decision making responds to these three forms of perturbation, expressed in chemical terms as rate parameters, stochasticity, and reaction topology. Remarkably, we found that there was no correlation between noise robustness and either of the others and only a weak correlation between robustness to parameters and topology. Thus, a given chemical switch could be robust to noise yet sensitive to parametric or topological changes. However, we found families of reaction topologies derived from a common core bistable with symmetric feedback loops, which retained bistability despite the removal of reactions or substantially changing parameters. We propose that evolution involving chemical switches must navigate a complex landscape involving multiple forms of robustness, and the only way for a given switch to have a systematic advantage in robustness is to come from a ‘good family’ of mirrorsymmetric topologies.

Significance Statement

Life endures despite metabolic fluctuations and environmental assaults. For the thousands of cellular decisions to continue to work, they must be robust to these perturbations. Many cellular decisions are made and stored by chemical switches, which like light switches retain their state – on or off – even after the trigger is gone. We computationally explored what makes chemical switches robust. It turns out that some are robust to thermal noise, others to mutations that disable part of the switch, or to changes in chemical conditions. Surprisingly, these different forms of robustness are mostly independent. However, chemical switches come in families built around core reactions, and these families tend to score high or low on several measures of robustness.
Adaptive laboratory evolution restores solvent tolerance in plasmid-curedPseudomonas putidaS12; a molecular analysis
Authors: Kusumawardhani Hadiastri , Furtwängler Benjamin , Blommestijn Matthijs , Kaltenytė Adelė , van der Poel Jaap , Kolk Jevan , Hosseini Rohola , de Winde Johannes H.
Published: August 2020

Pseudomonas putidaS12 is intrinsically solvent-tolerant and constitutes a promising platform for biobased production of aromatic compounds and biopolymers. The genome ofP. putidaS12 consists of a 5.8 Mbp chromosome, and a 580 kbp megaplasmid pTTS12 that carries several gene clusters involved in solvent tolerance. Removal of pTTS12 caused a significant reduction in solvent tolerance. In this study, we succeeded in restoring solvent tolerance in plasmid-curedP. putidaS12 using adaptive laboratory evolution (ALE), underscoring the innate solvent-tolerance of this strain.

Whole genome sequencing revealed several single nucleotide polymorphisms (SNPs) and a mobile element insertion, enabling ALE-derived strains to survive and sustain growth in the presence of a high toluene concentration (10% v/v). Mutations were identified in an RND efflux pump regulatorarpR, resulting in constitutive upregulation of the multifunctional efflux pump ArpABC. SNPs were also found in the intergenic region and subunits of ATP synthase, RNA polymerase subunit β’, global two-component regulatory system (GacA/GacS) and a putative AraC-family transcriptional regulator Afr. RNA-seq analysis further revealed a constitutive down-regulation of energy consuming activities in ALE-derived strains, including flagellar assembly, F0F1 ATP synthase, and membrane transport proteins. Out results indicate that constitutive expression of an alternative solvent extrusion pump in combination with high metabolic flexibility ensures restoration of solvent-tolerance inP. putidaS12 lacking its megaplasmid.