bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating the contribution of transmission in primary healthcare clinics to community-wide TB disease incidence, and the impact of infection prevention and control interventions, in KwaZulu-Natal, South Africa
Authors: McCreesh Nicky , Karat Aaron S , Govender Indira , Baisley Kathy , Diaconu Karin , Yates Tom A , Houben Rein MGJ , Kielmann Karina , Grant Alison D , White Richard G
Published: August 2021

Background

There is a high risk of Mycobacterium tuberculosis (Mtb) transmission in healthcare facilities in high burden settings. Recent World Health Organization guidelines on tuberculosis infection prevention and control (IPC) recommend a range of measures to reduce transmission in healthcare and institutional settings. These were evaluated primarily based on evidence for their effects on transmission to healthcare workers in hospitals. To estimate the overall impact of IPC interventions, it is necessary to also consider their impact on community-wide tuberculosis incidence and mortality.

Methods

We developed an individual-based model of Mtb transmission between household members, in primary healthcare clinics (PHCs), and in other congregate settings; drug sensitive and multidrug resistant tuberculosis disease development and resolution; and HIV and antiretroviral therapy (ART) and their effects on tuberculosis. The model was parameterised using data from a high HIV prevalence, rural/peri-urban community in KwaZulu-Natal, South Africa, including data on social contact in clinics and other settings by sex, age group, and HIV/ART status; and data on the prevalence of tuberculosis in clinic attendees and the general population. We estimated the proportion of disease in adults that resulted from transmission in PHC clinics in 2019, and the impact of a range of IPC interventions in clinics on community-wide TB incidence and mortality.

Results

We estimate that 7.6% (plausible range 3.9-13.9%) of drug sensitive and multidrug resistant tuberculosis in adults resulted from transmission in PHC clinics in the study community in 2019. The proportion is higher in HIV-positive people, at 9.3% (4.8%-16.8%), compared to 5.3% (2.7%-10.1%) in HIV-negative people. We estimate that IPC interventions could reduce the number of incident TB cases in the community in 2021-2030 by 3.4-8.0%, and the number of deaths by 3.0-7.2%.

Conclusions

A non-trivial proportion of tuberculosis results from transmission in PHC clinics in the study communities, particularly in HIV-positive people. Implementing IPC interventions could lead to moderate reductions in disease burden. We therefore recommend that IPC measures in clinics should be implemented both for their benefits to staff and patients, but also for their likely effects on TB incidence and mortality in the surrounding community.
A Sustainable Development Goal framework to guide multisectoral action on NAFLD through a societal approach
Authors: Lazarus Jeffrey V , Mark Henry E , Colombo Massimo , Demaio Sandro , Dillon John F , George Jacob , Hagström Hannes , Hocking Samantha , Lee Nancy , Nieuwenhuijsen Mark J , Rinella Mary E , Romero-Gomez Manuel , Soriano Joan B , Schattenberg Jörn M , Tacke Frank , Tsochatzis Emmanuel A. , Valenti Luca , Zelber-Sagi Shira , Dirac M. Ashworth , Huang Terry T-K
Published: August 2021

Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent condition that requires a comprehensive and coordinated response across sectors and disciplines. In the absence of a multisectoral framework, we developed a NAFLD-Sustainable Development Goals (SDG) framework to converge thinking about the design and delivery of NAFLD public health responses. A multidisciplinary group identified SDG targets and indicators for inclusion in the NAFLD-SDG framework through a two-stage process. Firstly, a core team of three researchers independently reviewed the 169 SDG targets and 231 unique indicators proposed by the Inter-Agency and Expert Group on SDG to select a shortlist. Over two Delphi rounds, a multidisciplinary group of 12 experts selected which of the shortlisted targets and indicators to include in the NAFLD-SDG framework. Respondents also provided written feedback on their selection. Targets and indicators with 75% or greater agreement were included in the final NAFLD-SDG framework. The final framework comprises 16 targets–representing 9% of all SDG targets and 62% (16/26) of the shortlisted targets–and seven indicators, accounting for 50% (7/14) of the shortlisted indicators and 3% of all SDG indicators. The selected targets and indicators cover a broad range of factors, from health, food and nutrition to education, the economy and the built environment. Addressing the challenge of NAFLD will require re-envisioning the liver health landscape, with a greater focus on joined-up systems thinking and action. The NAFLD-SDG framework can help guide this process, including by outlining the key stakeholders with whom the liver health community needs to engage.
Association of chronic kidney disease, ethnicity and socioeconomic status with COVID-19 hospitalisation and mortality: a UK Biobank study
Authors: Wilkinson Thomas J , Lightfoot Courtney J , Smith Alice C. , Yates Thomas , Khunti Kamlesh , Zaccardi Francesco
Published: August 2021

In individuals with chronic kidney disease (CKD), Black and South Asian ethnic groups are twice as likely to have severe COVID-19 compared to White participants, whilst the most socially deprived groups are at a 50-60% increased risk of severe COVID-19.

This study is the first to highlight the association between ethnicity and socioeconomic deprivation and the risk of severe COVID-19 among those with CKD in the UK.

Interventions to reduce morbidity and mortality amongst these groups and policy and practice improvements are needed to address the broad disparity among CKD patients.
The cost of illness for childhood clinical pneumonia and invasive pneumococcal disease in Nigeria
Authors: Adamu Aishatu L , Karia Boniface , Bello Musa M , Jahun Mahmoud G , Gambo Safiya , Ojal John , Scott J Anthony A G , Jemutai Julie , Adetifa Ifedayo M O
Published: August 2021

Background: Pneumococcal disease contributes significantly to childhood morbidity and mortality and treatment is costly. Nigeria recently introduced the Pneumococcal Conjugate Vaccine (PCV) to prevent pneumococcal disease. The aim of this study is to estimate health provider and household costs for the treatment of pneumococcal disease in children aged <5 years (U5s), and to assess the impact of these costs on household income.

Methods: We recruited U5s with clinical pneumonia, pneumococcal meningitis or pneumococcal septicaemia from a tertiary and a secondary level hospital in Kano, Nigeria. We obtained resource utilisation data from medical records to estimate costs of treatment to provider, and household expenses and income loss data from caregiver interviews to estimate costs of treatment to households. We defined catastrophic health expenditure (CHE) as household costs exceeding 25% of monthly household income and estimated the proportion of households that experienced it. We compared CHE across tertiles of household income (from the poorest to least poor).

Results: Of 480 participants recruited, 244 had outpatient pneumonia, and 236 were hospitalised with pneumonia (117), septicaemia (66) and meningitis (53). Median (IQR) provider costs were US$17 (US$14-22) for outpatients and US$272 (US$271-360) for inpatients. Median household cost was US$51 (US$40-69). Overall, 33% of households experienced CHE, while 53% and 4% of the poorest and least poor households, experienced CHE respectively. The odds of CHE increased with admission at the secondary hospital, a diagnosis of meningitis or septicaemia, higher provider costs, and caregiver having a non-salaried job.

Conclusion: Provider costs are substantial, and households incur treatment expenses that considerably impact on their income and this is particularly so for the poorest households. Sustaining the PCV programme and ensuring high and equitable coverage to lower disease burden will reduce the economic burden of pneumococcal disease to the healthcare provider and households.
SARS-CoV-2 antibody binding and neutralization in dried blood spot eluates and paired plasma
Authors: Itell Hannah L. , Weight Haidyn , Fish Carolyn S. , Logue Jennifer K. , Franko Nicholas , Wolf Caitlin R. , McCulloch Denise J. , Galloway Jared , Matsen Frederick A. , Chu Helen Y. , Overbaugh Julie
Published: August 2021

Widescale assessment of SARS-CoV-2-specific antibodies is critical to understanding population seroprevalence, correlates of protection, and the longevity of vaccine-elicited responses. Most SARS-CoV-2 studies characterize antibody responses in plasma/sera. While reliable and broadly used, these samples pose several logistical restrictions such as requiring venipuncture for collection and cold chain for transportation and storage. Dried blood spots (DBS) overcome these barriers as they can be self-collected by fingerstick and mailed and stored at ambient temperature. Here, we evaluate the suitability of DBS for SARS-CoV-2 antibody assays by comparing several antibody responses between paired plasma and DBS from SARS-CoV-2 convalescent and vaccinated individuals. We found that DBS not only reflected plasma antibody binding by ELISA and epitope profiles using phage-display, but also yielded SARS-CoV-2 neutralization titers that highly correlated with paired plasma. Neutralization measurement was further streamlined by adapting assays to a high-throughput 384-well format. This study supports the adoption of DBS for numerous SARS-CoV-2 binding and neutralization assays.
Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector
Authors: Haas Brian J. , Dobin Alexander , Ghandi Mahmoud , Van Arsdale Anne , Tickle Timothy , Robinson James T. , Gillani Riaz , Kasif Simon , Regev Aviv
Published: August 2021

Motivation

Gene fusions play a key role as driver oncogenes in tumors, and their reliable discovery and detection are important for cancer research, diagnostics, prognostics and guiding personalized therapy. While discovering gene fusions from genome sequencing can be laborious and costly, the resulting “fusion transcripts” can be recovered from RNA-seq data of tumor and normal samples. However, alleged and putative fusion transcripts can also arise from multiple sources other than chromosomal rearrangements, including cis- or trans-splicing events, experimental artifacts during RNA-seq or computational errors of transcriptome reconstruction methods. Understanding how to discern, interpret, categorize, and verify predicted fusion transcripts is essential for consideration in clinical settings and prioritization for further research.

Here, we present FusionInspector for in silico characterization and interpretation of candidate fusion transcripts from RNA-seq and exploration of their sequence and expression characteristics. We applied FusionInspector to thousands of tumor and normal transcriptomes, and identified statistical and experimental features enriched among biologically impactful fusions. Through clustering and machine learning, we identified large collections of fusions potentially relevant to tumor and normal biological processes. We show that biologically relevant fusions are enriched for relatively high expression of the fusion transcript, imbalanced fusion allelic ratios, and canonical splicing patterns, and are deficient in sequence microhomologies detected between partner genes. We demonstrate that FusionInspector accurately validates fusion transcripts in silico, and helps identify and characterize numerous understudied fusions in tumor and normal tissues samples. FusionInspector is freely available as open source for screening, characterization, and visualization of candidate fusions via RNA-seq, and helps with transparent explanation and interpretation of machine learning predictions and their experimental sources.

Highlights

FusionInspector software for supervised analysis of candidate fusion transcripts

Clustering of recurrent fusion transcripts resolves biologically relevant fusions

Identification of distinguishing characteristics of known and novel fusion transcripts in tumor and normal tissues
The Ca2+ concentration in vitro impacts the cytokine production of mouse and human lymphoid cells and the polarization of human macrophages
Authors: Eskiocak Yusuf Cem , Ayyildiz Zeynep Ozge , Gunalp Sinem , Korkmaz Asli , Helvaci Derya Goksu , Dogan Yavuz , Sag Duygu , Wingender Gerhard
Published: August 2021

Various aspects of the in vitro culture conditions can impact the functional response of immune cells. For example, it was shown that a Ca2+ concentration of at least 1.5 mM during in vitro stimulation is needed for optimal cytokine production by conventional αβ T cells. Here we extend these findings by showing that also unconventional T cells (invariant Natural Killer T cells, mucosal-associated invariant T cells, γδ T cells), as well as B cells, show an increased cytokine response following in vitro stimulation in the presence of elevated Ca2+ concentrations (approx. 1.8 mM). This effect appeared more pronounced with mouse than with human lymphoid cells and did not influence their survival. A similarly increased cytokine response due to elevated Ca2+ levels was observed with primary human monocytes. In contrast, primary human monocyte-derived macrophages, either unpolarized (M0) or polarized into M1 or M2 macrophages, displayed increased cell death in the presence of elevated Ca2+ concentrations. Furthermore, elevated Ca2+ concentrations promoted phenotypic M1 differentiation by increasing M1 markers on M1 and M2 macrophages and decreasing M2 markers on M2 macrophages. However, the cytokine production of macrophages, again in contrast to the lymphoid cells, was unaltered by the Ca2+ concentration. In summary, our data demonstrate that the Ca2+ concentration during in vitro cultures is an important variable to be considered for functional experiments and that elevated Ca2+ levels can boost cytokine production by both mouse and human lymphoid cells.
Biomorphogenic feedbacks and the spatial organisation of a dominant grass steer dune development
Authors: Bonte Dries , Batsleer Femke , Provoost Sam , Reijers Valérie , Vandegehuchte Martijn L. , Van De Walle Ruben , Dan Sebastian , Matheve Hans , Rauwoens Pieter , Strypsteen Glenn , Suzuki Tomohiro , Verwaest Toon , Hillaert Jasmijn
Published: August 2021

Nature-based solutions to mitigate the impact of future climate change depend on restoring biological diversity and natural processes. Coastal foredunes represent the most important natural flood barriers along coastlines worldwide, but their area has been squeezed dramatically because of a continuing urbanisation of coastlines, especially in Europe. Dune development is steered by the development of vegetation in interaction with sand fluxes from the beach. Marram grass (Calamagrostis arenaria, formerlyAmmophila arenaria) is the main dune building species along most European coasts, but also in other continents where the species was introduced. Engineering of coastal dunes, for instance by building dunes in front of dikes, needs to be based on a solid understanding of the species’ interactions with the environment. Only quantitative approaches enable the further development of mechanistic models and coastal management strategies that encapsulate these biomorphogenic interactions. We here provide a quantitative review of the main biotic and physical interactions that affect marram grass performance, their interactions with sand fluxes and how they eventually shape dune development. Our review highlights that the species’ spatial organisation is central to dune development. We further demonstrate this importance by means of remote sensing and a mechanistic model and provide an outlook for further research on the use of coastal dunes as a nature-based solution for coastal protection.
Controlled Administration of Dehydrochloromethyltestosterone in Humans: Urinary Excretion and Long-Term Detection of Metabolites for Anti-Doping Purpose
Authors: Loke Steffen , de la Torre Xavier , Iannone Michele , Piana Giuseppe La , Schlörer Nils , Botrè Francesco , Bureik Matthias , Parr Maria Kristina
Published: August 2021

Dehydrochloromethyltestosterone (DHCMT) is an anabolic-androgenic steroid that was developed by Jenapharm in the 1960s and was marketed as Oral Turinabol®. It is prohibited in sports at all times; nevertheless, there are several findings by anti-doping laboratories every year. New long-term metabolites have been proposed in 2011/12, which resulted in adverse analytical findings in retests of the Olympic games of 2008 and 2012. However, no controlled administration trial monitoring these long-term metabolites was reported until now. In this study, DHCMT (5 mg, p.o.) was administered to five healthy male volunteers and their urine samples were collected for a total of 60 days. The unconjugated and the glucuronidated fraction were analyzed separately by gas chromatography coupled to tandem mass spectrometry. The formation of the described long-term metabolites was verified, and their excretion monitored in detail.

Due to interindividual differences there were several varieties in the excretion profiles among the volunteers. The metabolite M3, which has a fully reduced A-ring and modified D-ring structure, was identified by comparison with reference material as 4α-chloro-17β-hydroxymethyl-17α-methyl-18-nor-5α-androstan-13-en-3α-ol. It was found to be suitable as long-term marker for the intake of DHCMT in four of the volunteers. In one of the volunteers, it was detectable for 45 days after single oral dose administration. However, in two of the volunteers M5 (already published as long-term metabolite in the 1990s) showed longer detection windows. In one volunteer M3 was undetectable but another metabolite, M2, was found as the longest detectable metabolite.

The last sample clearly identified as positive was collected between 9.9 and 44.9 days. Furthermore, the metabolite epiM4 (partially reduced A-ring and a modified D-ring structure which is epimerized in position 17 compared to M3) was identified in the urine of all volunteers with the help of chemically synthesized reference as 4-chloro-17α-hydroxymethyl-17β-methyl-18-nor-androsta-4,13-dien-3β-ol. It may serve as additional confirmatory metabolite.

It is highly recommended to screen for all known metabolites in both fractions, glucuronidated and unconjugated, to improve identification of cheating athletes. This study also offers some deeper insights into the metabolism of DHCMT and of 17α-methyl steroids in general.
Dynamic Cognitive States Predict Individual Variability in Behavior and Modulate with EEG Functional Connectivity during Working Memory
Authors: Beauchene Christine , Hinault Thomas , Sarma Sridevi V. , Courtney Susan
Published: August 2021

Fluctuations in strategy, attention, or motivation can cause large variability in performance across task trials. Typically, this variability is treated as noise, and assumed to cancel out, leaving supposedly stable relationships among behavior, neural activity, and experimental task conditions. Those relationships, however, could change with a participant’s internal cognitive states, and variability in performance may carry important information regarding those states, which cannot be directly measured. Therefore, we used a mathematical, state-space modeling framework to estimate internal states from measured behavioral data, quantifying each participant’s sensitivity to factors such as past errors or distractions, to predict their reaction time fluctuations. We show how modeling these states greatly improves trial-by-trial prediction of behavior. Further, we identify EEG functional connectivity features that modulate with each state. These results illustrate the potential of this approach and how it could enable quantification of intra- and inter-individual differences and provide insight into their neural bases.

Statement of Relevance

Cognitive behavioral performance and its neural bases vary both across individuals and within individuals over time. Understanding this variability may be key to the success of clinical or educational interventions. Internal cognitive states reflecting differences in strategy, attention, and motivation may drive much of these inter- and intra-individual differences, but often cannot be reliably controlled or measured in cognitive neuroscience research. The mathematical modeling framework developed here uses measured data to estimate a participant’s dynamic, internal cognitive states, with each state derived from specific factors hypothesized to affect attention, motivation or strategy. The results highlight potential sources of behavioral variability and reveal EEG features that modulate with each state. Our method quantifies and characterizes individual behavioral differences and highlights their underlying neural mechanisms, which could be used for future targeted training or neuromodulation therapies to improve cognitive performance.
Rapid Prototyping of Cell Culture Microdevices Using Parylene-Coated 3D Prints
Authors: O’Grady Brian J. , Geuy Michael D. , Kim Hyosung , Balotin Kylie M. , Allchin Everett R. , Florian David C. , Bute Neelansh N. , Scott Taylor E. , Lowen Gregory B. , Fricker Colin M. , Guelcher Scott A. , Wikswo John P. , Bellan Leon M. , Lippmann Ethan S.
Published: August 2021

Fabrication of microfluidic devices by photolithography generally requires specialized training and access to a cleanroom. As an alternative, 3D printing enables cost-effective fabrication of microdevices with complex features that would be suitable for many biomedical applications. However, commonly used resins are cytotoxic and unsuitable for devices involving cells. Furthermore, 3D prints are generally refractory to elastomer polymerization such that they cannot be used as master molds for fabricating devices from polymers (e.g. polydimethylsiloxane, or PDMS). Different post-print treatment strategies, such as heat curing, ultraviolet light exposure, and coating with silanes, have been explored to overcome these obstacles, but none have proven universally effective. Here, we show that deposition of a thin layer of parylene, a polymer commonly used for medical device applications, renders 3D prints biocompatible and allows them to be used as master molds for elastomeric device fabrication. When placed in culture dishes containing human neurons, regardless of resin type, uncoated 3D prints leached toxic material to yield complete cell death within 48 hours, whereas cells exhibited uniform viability and healthy morphology out to 21 days if the prints were coated with parylene. Diverse PDMS devices of different shapes and sizes were easily casted from parylene-coated 3D printed molds without any visible defects. As a proof-of-concept, we rapid prototyped and tested different types of PDMS devices, including triple chamber perfusion chips, droplet generators, and microwells. Overall, we suggest that the simplicity and reproducibility of this technique will make it attractive for fabricating traditional microdevices and rapid prototyping new designs. In particular, by minimizing user intervention on the fabrication and post-print treatment steps, our strategy could help make microfluidics more accessible to the biomedical research community.
Rescue of behavioral and electrophysiological phenotypes in a Pitt-Hopkins syndrome mouse model by genetic restoration of Tcf4 expression
Authors: Kim Hyojin , Gao Eric B. , Draper Adam , Berens Noah C. , Vihma Hanna , Zhang Xinyuan , Higashi-Howard Alexandra , Ritola Kimberly D. , Simon Jeremy M. , Kennedy Andrew J. , Philpot Benjamin D.
Published: August 2021

Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by monoallelic mutation or deletion in the transcription factor 4 (TCF4) gene. Individuals with PTHS typically present in the first year of life with developmental delay and exhibit intellectual disability, lack of speech, and motor incoordination. There are no effective treatments available for PTHS, but the root cause of the disorder, TCF4 haploinsufficiency, suggests that it could be treated by normalizing TCF4 gene expression. Here we performed proof-of-concept viral gene therapy experiments using a conditional Tcf4 mouse model of PTHS and found that postnatally reinstating Tcf4 expression in neurons improved anxiety-like behavior, activity levels, innate behaviors, and memory. Postnatal reinstatement also partially corrected EEG abnormalities, which we characterized here for the first time, and the expression of key TCF4-regulated genes. Our results support a genetic normalization approach as a treatment strategy for PTHS, and possibly other TCF4-linked disorders.
QT-AMP: Quanti-Tray-based amplicon sequencing for simultaneous quantification and identification of enterococci for microbial source tracking
Authors: Urakawa Hidetoshi , Hancock Taylor L. , Kratz Michael A. , Armstrong Rick A.
Published: August 2021

Enterococcus is ubiquitous in human feces and has been adopted as a useful indicator of human fecal pollution in water. Although regular enterococci monitoring only examines their numbers, identification of human-specific Enterococcus species or genotypes could help in the discrimination of human fecal contamination from other environmental sources. We documented a new approach to characterize enterococci using an amplicon sequencing platform from Quanti Trays after following the counting of most probable numbers (MPN) of enterococci. We named this method as QT-AMP (Quanti-Tray-based amplicon sequencing). We tested surface water samples collected from three rivers in southwest Florida. We detected 11 Enterococcus species from 45 samples in 1.1 million sequence reads. The method detected three rare species and eight cosmopolitan species (Enterococcus faecalis, E.faecium, E. casseliflavus, E. hirae, E. mundtii, E. gallinarum, E. avium, and E. durans) which have been commonly documented in various enterococci isolation studies. It is likely that the approximate detection level of QT-AMP is four orders of magnitude higher than regular 16S rRNA gene amplicon sequencing. QT-AMP revealed that a majority of Enterolert positive signals are actually the mixture of both enterococci and other facultative aerobes and anaerobes. QT-AMP may have the potential to monitor not only enterococci but also other pathogenic bacteria commonly found in natural environments. This QT-AMP could be a powerful tool to streamline the quantification and identification of enterococci and allows us to do more accurate and efficient microbial source tracking in various water management projects and human health risk assessment.

Highlights

A selected primer set (27f-519r) can differentiate over 50 Enterococcus species and is suitable for Illumina amplicon sequencing.

The median of the relative contribution of enterococci reads among total sequencing reads was 82.7% and ranged between 0% and 100%.

Enterolert signals are most likely the mixture of enterococci and other facultative aerobes and anaerobes.

We identified eight cosmopolitan enterococci species and three rare species.

The median of the relative contribution of non-enterococci reads among total sequencing reads was 17.3%, respectively, and ranged between 0% and 100%.
Event-Related Phase Synchronization Propagates Rapidly across Human Ventral Visual Cortex
Authors: Woolnough Oscar , Forseth Kiefer J. , Rollo Patrick S. , Roccaforte Zachary J. , Tandon Nitin
Published: August 2021

Visual inputs to early visual cortex integrate with semantic, linguistic and memory inputs in higher visual cortex, in a manner that is rapid and accurate, and enables complex computations such as face recognition and word reading. This implies the existence of fundamental organizational principles that enable such efficiency. To elaborate on this, we performed intracranial recordings in 82 individuals while they performed tasks of varying visual and cognitive complexity. We discovered that visual inputs induce highly organized posterior-to-anterior propagating patterns of phase modulation across the ventral occipitotemporal cortex. At individual electrodes there was a stereotyped temporal pattern of phase progression following both stimulus onset and offset, consistent across trials and tasks. The phase of low frequency activity in anterior regions was predicted by the prior phase in posterior cortical regions. This spatiotemporal propagation of phase likely serves as a feed-forward organizational influence enabling the integration of information across the ventral visual stream. This phase modulation manifests as the early components of the event related potential; one of the most commonly used measures in human electrophysiology. These findings illuminate fundamental organizational principles of the higher order visual system that enable the rapid recognition and characterization of a variety of inputs.
Predictive framework of macrophage activation
Authors: Sanin David E. , Ge Yan , Marinkovic Emilija , Kabat Agnieszka M. , Castoldi Angela , Caputa George , Grzes Katarzyna M. , Curtis Jonathan D. , Willenborg Sebastian , Dichtl Stefanie , Reinhardt Susanne , Dahl Andreas , Pearce Erika L. , Eming Sabine A. , Gerbaulet Alexander , Roers Axel , Murray Peter J. , Pearce Edward J.
Published: August 2021

Macrophages populate every organ during homeostasis and disease, displaying features of tissue imprinting and heterogeneous activation. The disjointed picture of macrophage biology that emerged from these observations are a barrier for integration across models or within vitromacrophage activation paradigms. We set out to contextualize macrophage heterogeneity across mouse tissues and inflammatory conditions, specifically aiming to define a common framework of macrophage activation. We built a predictive model with which we mapped the activation of macrophages across 12 tissues and 25 biological conditions, finding a striking commonality and finite number of transcriptional profiles, which we modelled as defined stages along four conserved activation paths. We verified this model with adoptive cell transfer experiments and identified transient RELMɑ expression as a feature of macrophage tissue engraftment. We propose that this integrative approach of macrophage classification allows the establishment of a common predictive framework of macrophage activation in inflammation and homeostasis.

One Sentence Summary

We propose an integrative approach of macrophage classification that allows the establishment of a common framework of macrophage activation in inflammation and homeostasis.
Broadening the toolkit for quantitatively evaluating noncanonical amino acid incorporation in yeast
Authors: Stieglitz J.T. , Potts K.A. , Van Deventer J.A.
Published: August 2021

Genetic code expansion is a powerful approach for advancing critical fields such as biological therapeutic discovery. However, the machinery for genetically encoding noncanonical amino acids (ncAAs) is only available in limited plasmid formats, constraining potential applications. In extreme cases, the introduction of two separate plasmids, one containing an orthogonal translation system (OTS) to facilitate ncAA incorporation and a second for expressing a ncAA-containing protein of interest, is not possible due to lack of convenient selection markers. One strategy to circumvent this challenge is to express the OTS and protein of interest from a single vector. For what we believe is the first time in yeast, we describe here several sets of single plasmid systems (SPSs) for performing genetic code manipulation and compare the ncAA incorporation capabilities of these plasmids against the capabilities of previously described dual plasmid systems (DPSs). For both dual fluorescent protein reporters and yeast display reporters tested with multiple OTSs and ncAAs, measured ncAA incorporation efficiencies with SPSs were determined to be equal to or improved relative to efficiencies determined with DPSs. Click chemistry on yeast cells displaying ncAA-containing proteins was also shown to be feasible in both formats, although differences in reactivity between formats suggest the need for caution when using such approaches. Additionally, we investigated whether these reporters would support separation of yeast strains known to exhibit distinct ncAA incorporation efficiencies. Model sorts conducted with mixtures of two strains transformed with the same SPS or DPS led to enrichment of a strain known to support higher efficiency ncAA incorporation, suggesting that these reporters will be suitable for conducting screens for strains exhibiting enhanced ncAA incorporation efficiencies. Overall, our results confirm that SPSs are well-behaved in yeast and provide a convenient alternative to DPSs. In particular, SPSs are expected to be invaluable for conducting high-throughput investigations of the effects of genetic or genomic changes on ncAA incorporation efficiency and, more fundamentally, the eukaryotic translation apparatus.

Abstract Figure
A role of cryptochrome for magnetic field-dependent improvement of sleep quality, lifespan and motor function in Drosophila
Authors: Kawasaki Haruhisa , Okano Hideyuki , Ishiwatari Hiromi , Kishi Tetsuo , Ishida Norio
Published: August 2021

Understanding the molecular genetic basis of animal magnet reception has been one of the big challenges in biology. Recently it was discovered that the magnetic sense of Drosophila melanogaster is mediated by the ultraviolet (UV)-A/blue light photoreceptor cryptochrome (Cry).

Here, using the fruit fly as a magnet receptive model organism, we show that exposure to a specific AC magnetic field during night time affected the health of the fly. AC magnetic field exposure showed lifespan extension under starvation, sleep improvement and prevention of decreased motor function. In contrast, all the health improvement effect was not observed in cryptochrome mutant flies (cryb). We showed that AC magnetic field exposure prevented motor dysfunction in Gaucher’s disease model Drosophila. The data suggests that magnetic field-dependent improvement of sleep quality, lifespan and motor function is mediated through a cry-dependent pathway in animals.
Comparative analysis of post-vaccination anti-spike IgG antibodies in old Nursing Home Residents and in middle-aged Healthcare workers
Authors: Jeulin H. , Craus D. , Labat C. , Benetos A.
Published: August 2021

The current consensus is that 2 doses of mRNA vaccines against SARS-CoV-2 are needed for people without COVID-19 history, while for those who had suffered COVID-19, a single dose may be enough to achieve high levels of immunization. This consensus has been based on results obtained in middle-aged populations, whereas only few data exist for the oldest and most frail adults such as nursing home residents (NH-Res) that is, the population most vulnerable to develop severe forms of COVID-19.

In this study, we studied the anti-SARS-CoV-2 IgG(S) level of NH-Res and healthcare workers (HCWs) with or without a history of COVID-19 infection taking into account the time since immunization (COVID-19 and/or vaccination). 654 subjects were analyzed: 397 NH-Res (median age 88, IQR 82-93 years, 75% women) and 257 Health Care Workers (HCWs, median 46, IQR 38-54 years, 81% women). NH-Res and HCWs were classified in one of the following 3 groups: No-COVID history and 2 vaccine shots (COV-NO/2VACC); Yes-COVID history and 1 (COV-YES/1VACC) or 2 (COV-YES/2VACC) vaccine injections.

The time-related decrease in IgG (S) in subjects without COVID-19 history, SARS-COV-2 serology would be negative in HCWs approximately 220 days and in residents 180 days after vaccination. This time-related decrease was much slower in those with history of COVID. NH-Res belonging into the COV-NO/2VACC and the COV-YES/1VACC groups showed lower IgG (S) levels than the same groups of HCWs (for both groups, p<0.0001), whereas in the group COV-YES/2VACC, IgG (S) levels were similar in NH-Res and HCWs (p=0.88). These results remained unchanged after adjustment for age and duration since immunization. Thus, in NH-Res, 2 vaccine shots were associated with a more pronounced immune response, whereas in HCWs, 1 or 2 vaccine shots in patients with COVID-19 history did make any difference. These results indicate significant differences in mRNA vaccination between NH-Res and middle-aged controls, and could contribute to the specification of vaccine policy in this very old, frail population.
Azithromycin in patients with Covid-19; a systematic review and metanalysis
Authors: Ayerbe Luis , Forgone Ivo , Risco-Risco Carlos , Pérez-Piñar Maria , Ayis Salma
Published: August 2021

Background

Azithromycin (AZM) has been widely used in the management of Covid-19. However, the evidence on its actual effects remains disperse and difficult to apply in clinical settings. This systematic review and metanalysis summarizes the available evidence to date on the beneficial and adverse effect of AZM in patients with Covid-19.

Methods

The PRISMA 2020 statement criteria were followed. Randomized controlled trials (RCTs) and observational studies comparing clinical outcomes of patients treated, and not treated, with AZM, indexed until the 5th of July 2021, were searched in PubMed, Embase, The Web of Science, Scopus, The Cochrane Central Register of Controlled Trials, and MedRXivs. We used Random-effects models to estimate pooled effect size from aggregate data.

Results

The initial search produced 4950 results. Finally, 16 studies, five RCTs and 11 with an observational design, with a total of 22984 patients, were included. The metanalysis showed no difference in mortality for those treated, or not, with AZM, OR: 0.95 (0.79-1.13). There was also no significant difference for those treated, and not, with AZM in need for hospital admission or time to admission from ambulatory settings, clinical severity, need for intensive care, or adverse effects.

Conclusions

These results presented in this review do not support the use of AZM in the management of Covid-19. They also show that any harm caused to the patient who received it is unlikely. Future research on treatment for patients with Covid-19 may need to focus on other drugs.
Functional non-coding SNPs in human endothelial cells fine-map vascular trait associations
Authors: Toropainen Anu , Stolze Lindsey K. , Örd Tiit , Whalen Michael , Martí Torrell Paula , Link Verena M. , Kaikkonen Minna U , Romanoski Casey
Published: August 2021

Functional consequences of genetic variation in the non-coding human genome are difficult to ascertain despite demonstrated associations to common, complex disease traits. To elucidate properties of functional non-coding SNPs with effects in human endothelial cells (EC), we utilized molecular Quantitative Trait Locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation to nominate a set of likely functional non-coding SNPs. Together with information from genome-wide association studies for vascular disease traits, we tested the ability of 34,344 variants to perturb enhancer function in ECs using the highly multiplexed STARR-seq assay. Of these, 5,592 variants validated, whose enriched attributes included: 1) mutations to TF binding motifs for ETS or AP1 that are regulators of EC state, 2) location in accessible and H3K27ac-marked EC chromatin, and 3) molQTLs associations whereby alleles associate with differences in chromatin accessibility and TF binding across genetically diverse ECs. Next, using pro-inflammatory IL1B as an activator of cell state, we observed robust evidence (>50%) of context-specific SNP effects, underscoring the prevalence of non-coding gene-by-environment (GxE) effects. Lastly, using these cumulative data, we fine-mapped vascular disease loci and highlight evidence suggesting mechanisms by which non-coding SNPs at two loci affect risk for Pulse Pressure/Large Artery Stroke, and Abdominal Aortic Aneurysm through respective effects on transcriptional regulation of POU4F1 and LDAH. Together, we highlight the attributes and context dependence of functional non-coding SNPs, and provide new mechanisms underlying vascular disease risk.
Two-dimensional multiplexed assay for rapid and deep SARS-CoV-2 serology profiling and for machine learning prediction of neutralization capacity
Authors: Koide Akiko , Panchenko Tatyana , Wang Chan , Thannickal Sara A. , Romero Larizbeth A. , Teng Kai Wen , Li Francesca-Zhoufan , Akkappedi Padma , Corrado Alexis D. , Caro Jessica , Diefenbach Catherine , Samanovic Marie I. , Mulligan Mark J. , Hattori Takamitsu , Stapleford Kenneth A. , Li Huilin , Koide Shohei
Published: August 2021

Antibody responses serve as the primary protection against SARS-CoV-2 infection through neutralization of viral entry into cells. We have developed a two-dimensional multiplex bead binding assay (2D-MBBA) that quantifies multiple antibody isotypes against multiple antigens from a single measurement. Here, we applied our assay to profile IgG, IgM and IgA levels against the spike antigen, its receptor-binding domain and natural and designed mutants. Machine learning algorithms trained on the 2D-MBBA data substantially improve the prediction of neutralization capacity against the authentic SARS-CoV-2 virus of serum samples of convalescent patients. The algorithms also helped identify a set of antibody isotype–antigen datasets that contributed to the prediction, which included those targeting regions outside the receptor-binding interface of the spike protein. We applied the assay to profile samples from vaccinated, immune-compromised patients, which revealed differences in the antibody profiles between convalescent and vaccinated samples. Our approach can rapidly provide deep antibody profiles and neutralization prediction from essentially a drop of blood without the need of BSL-3 access and provides insights into the nature of neutralizing antibodies. It may be further developed for evaluating neutralizing capacity for new variants and future pathogens.
Transcranial magnetic stimulation of the occipital cortex interferes with foot movements in acquired but not congenitally blind individuals
Authors: Ikegami Tsuyoshi , Miura Gen , Hirashima Masaya , Naito Eiichi , Hirose Satoshi
Published: August 2021

Research has shown that the occipital cortex can be reorganized and repurposed for nonvisual perception and cognitive functions following visual loss in blind individuals. However, no studies have directly examined the involvement of the visual cortex in motor function. Here, we show that a rhythmic foot movement performed by acquired blind individuals can be disrupted by transcranial magnetic stimulation (TMS) to their primary and secondary visual cortex (V1/V2). This disruptive effect was absent for congenitally blind or sighted individuals. As a control, TMS to the neck muscles of acquired blind individuals confirms that this disruptive effect was not caused solely by the sensory (tactile/auditory) sensations accompanying the stimulation. Our results provide the direct evidence that functional repurposing of the human visual cortex is not restricted to perception and cognitive functions but also extends to motor function. Moreover, our findings suggest the nessecity of the visual experience before visual loss for the functional reorganization of the visual cortex for motor function.
Cell type-specific biotin labeling in vivo resolves regional neuronal proteomic differences in mouse brain
Authors: Rayaprolu Sruti , Bitarafan Sara , Betarbet Ranjita , Sunna Sydney , Cheng Lihong , Xiao Hailian , Bagchi Pritha , Duong Duc M. , Nelson Ruth , Goettemoeller Annie M. , Oláh Viktor János , Rowan Matt , Levey Allan I. , Wood Levi B. , Seyfried Nicholas T. , Rangaraju Srikant
Published: August 2021

Isolation and proteomic profiling of brain cell types, particularly neurons, pose several technical challenges which limit our ability to resolve distinct cellular phenotypes in neurological diseases. Therefore, we generated a novel mouse line that enables cell type-specific expression of a biotin ligase, TurboID, via Cre-lox strategy for in vivo proximity-dependent biotinylation of proteins. Using adenoviral-based and transgenic approaches, we show striking protein biotinylation in neuronal cell bodies and axons throughout the mouse brain. We quantified more than 2,000 neuron-derived proteins following enrichment that mapped to numerous subcellular compartments. Synaptic, transmembrane transporters, ion channel subunits, and disease-relevant druggable targets were among the most significantly enriched proteins. Remarkably, we resolved brain region-specific proteomic profiles of Camk2a neurons with distinct functional molecular signatures and disease associations that may underlie regional neuronal vulnerability. Leveraging the neuronal specificity of this in vivo biotinylation strategy, we used an antibody-based approach to uncover regionally unique patterns of neuron-derived signaling phospho-proteins and cytokines, particularly in the cortex and cerebellum. Our work provides a proteomic framework to investigate cell type-specific mechanisms driving physiological and pathological states of the brain as well as complex tissues beyond the brain.
Controlling reversible cell differentiation for labor division in microbial consortia
Authors: Salzano Davide , Fiore Davide , di Bernardo Mario
Published: August 2021

We address the problem of regulating and keeping at a desired balance the relative numbers between cells exhibiting a different phenotype within a monostrain microbial consortium. We propose a strategy based on the use of external control inputs, assuming each cell in the community is endowed with a reversible, bistable memory mechanism. Specifically, we provide a general analytical framework to guide the design of external feedback control strategies aimed at balancing the ratio between cells whose memory is stabilized at either one of two equilibria associated to different cell phenotypes. We demonstrate the stability and robustness properties of the control laws proposed and validate them in silico by means of a realistic agent-based implementation enabling cooperative bioproduction in microbial consortia. The proposed control framework may be used to allow long term coexistence of different populations, with both industrial and biotechnological applications.
Cytokinin-CLAVATA crosstalk is an ancient mechanism regulating shoot meristem homeostasis in land plants
Authors: Cammarata Joseph , Farfan Christopher Morales , Scanlon Michael , Roeder Adrienne HK
Published: August 2021

Plant shoots grow from stem cells within Shoot Apical Meristems (SAMs), which produce lateral organs while maintaining the stem cell pool. In the model flowering plant Arabidopsis, the CLAVATA (CLV) pathway functions antagonistically with cytokinin signaling to control the size of the multicellular SAM via negative regulation of the stem cell organizer WUSCHEL (WUS). Although comprising just a single cell, the SAM of the model moss Physcomitrium patens (formerly Physcomitrella) performs equivalent functions during stem cell maintenance and organogenesis, despite the absence of WUS-mediated stem cell organization. Our previous work showed that the stem cell-delimiting function of the CLV pathway receptors CLAVATA1 (CLV1) and RECEPTOR-LIKE PROTEIN KINASE2 (RPK2) is conserved in the moss P. patens. Here, we use P. patens to assess whether CLV-cytokinin crosstalk is also an evolutionarily conserved feature of stem cell regulation. Genetic analyses reveal that CLV1 and RPK2 regulate SAM proliferation via separate pathways in moss. Surprisingly, cytokinin receptor mutants also form ectopic stem cells in the absence of cytokinin signaling. Through modeling, we identified regulatory network archtectures that recapitulated the stem cell phenotypes of clv1 and rpk2 mutants, cytokinin application, cytokinin receptor mutations, and higher-order combinations of these perturbations. These models predict that CLV1 and RPK2 act through separate pathways wherein CLV1 represses cytokinin-mediated stem cell initiation and RPK2 inhibits this process via a separate, cytokinin-independent pathway. Our analysis suggests that crosstalk between CLV1 and cytokinin signaling is an evolutionarily conserved feature of SAM homeostasis that preceded the role of WUS in stem cell organization.