bluuebunny/crossref_metadata_2025 huggingface dataset:
SARS-CoV-2 Mortality Surveillance among Community Deaths brought to University Teaching Hospital Mortuary in Lusaka, Zambia, 2020
Authors: Hamukale Amos , Hines Jonas Z. , Sinyange Nyambe , Fwoloshi Sombo , Malambo Warren , Sivile Suilanji , Chanda Stephen , Mucheleng’anga Luchenga Adam , Kayeyi Nkomba , Himwaze Cordelia Maria , Shibemba Aaron , Leigh Tally , Mazaba Mazyanga L. , Kapata Nathan , Zulu Paul , Zyambo Khozya , Mupeta Francis , Agolory Simon , Mulenga Lloyd B. , Malama Kennedy , Kapina Muzala
Published: November 2021

Introduction

During March-December 2020, Zambia recorded 20,725 confirmed COVID-19 cases, with the first wave peaking between July and August. Of the 388 COVID-19-related deaths occurring nationwide, most occurred in the community. We report findings from COVID-19 mortality surveillance among community deaths brought to the University Teaching Hospital (UTH) mortuary in Lusaka.

Methods

In Zambia, when a person dies in the community, and is brought into a health facility mortuary, they are recorded as ‘brought in dead’ (BID). The UTH mortuary accepts persons BID for Lusaka District, the most populated district in Zambia. We analyzed data for persons BID at UTH during 2020. We analyzed two data sources: weekly SARS-CoV-2 test results for persons BID and monthly all-cause mortality numbers among persons BID. For all-cause mortality among persons BID, monthly deaths during 2020 that were above the upper bound of the 95% confidence interval for the historic mean (2017-2019) were considered significant. Spearman’s rank test was used to correlate the overall percent positivity in Zambia with all-cause mortality and SARS-CoV-2 testing among persons BID at UTH mortuary.

Results

During 2020, 7,756 persons were BID at UTH (monthly range 556-810). SARS-CoV-2 testing began in April 2020, and through December 3,131 (51.9%) of 6,022 persons BID were tested. Of these, 212 (6.8%) were SARS-CoV-2 positive with weekly percent test positivity ranging from 0-32%, with the highest positivity occurring during July 2020. There were 1,139 excess persons BID from all causes at UTH mortuary in 2020 compared to the 2017-2019 mean. The monthly number of persons BID from all causes was above the upper bound of the 95% confidence interval during June-September and December.

Conclusion

Increases in all-cause mortality and SARS-CoV-2 test positivity among persons BID at UTH mortuary corresponded with the first peak of the COVID-19 epidemic in June and August 2020, indicating possible increased mortality related to the COVID-19 epidemic in Zambia. Combining all-cause mortality and SARS-CoV-2 testing for persons BID provides useful information about the severity of the epidemic in Lusaka and should be implemented throughout Zambia.
COVID-19 in the Republic of Belarus: pandemic features and the interim safety and efficacy assessment of the Gam-COVID-Vac vaccine
Authors: Dashkevich Ala M , Vysotskaya Veronika S , Hlinskaya Iryna N , Skuranovich Anzhela L , Tarasenka Aliaksandr A , Karaban Inna A , Kolomiets Natalya D
Published: November 2021

Objective

To study the COVID-19 pandemic features among the population of the Republic of Belarus from February 2020 to September 2021 and assess the safety (tolerance) and epidemiological efficacy of the Gam-COVID-Vac vaccine (Sputnik V).

Materials and methods

A retrospective analysis of COVID-19 cases in the Republic of Belarus from the beginning of registration (February 28, 2020) to September 12, 2021 was performed. To assess the COVID-19 case detection dynamics, official registration data available on the website of the Ministry of Health of the Republic of Belarus were used.

Vaccine safety (tolerance) and efficacy were assessed in an observational study. Safety (tolerance) was assessed by presence/absence of adverse reactions: general and local ones.

The efficacy rate (E) and the epidemiological efficacy index (K) was calculated according to the formula: E(%)=100*(b-a)/b, K=b/a.

Results

Our data show that The COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: the first is the absence of COVID-19 cases in the country; the second is the registration of individual infection cases that came from abroad followed by local pathogen spread among the country’s population; the third is a local spread of COVID-19 among individuals who had contact with infected people; the fourth is the detection of cases where patients had no history of exposure to COVID-19 patients.

As of calendar week 26, 2021 Delta variant of SARS-CoV-2 has become the prevalent in the country.

Follow-up results in January-August 2021 showed that the Sputnik V vaccine was well tolerated, with 80,832 adverse reactions reported (2.99% (95% CI 2.9-3.0) of the total number of vaccine doses administered). In terms of severity, adverse reactions were mild (91.4% (95% CI 91.2-91.6)) and moderate (8.6% (95% CI 8.6-8.8)). The epidemiological efficacy rate was 96.3%, the epidemiological efficacy index was 26.7. Thus, the results obtained testify to high prophylactic efficacy of the Sputnik V vaccine.

Conclusions

The COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: from no cases in early 2020 to detected cases where most individuals had no history of contact with COVID-19 patients; periods of rising and falling incidence. The Sputnik V vaccine has demonstrated a high safety profile and epidemiological efficacy throughout mass vaccination in the Republic of Belarus.
Protocol for a cross-sectional study: Effects of a Multiple Sclerosis Relapse Therapy with Methylprednisolone on Offspring Neurocognitive Development and Behaviour (MS-Children)
Authors: Kozik Valeska , Schwab Matthias , Thiel Sandra , Hellwig Kerstin , Rakers Florian , Dreiling Michelle
Published: November 2021

Introduction

Multiple Sclerosis (MS) is the most common neuroimmunological disease in women of childbearing age. Current MS therapy consists of immunomodulatory relapse prevention with disease-modifying therapies (DMTs) and acute relapse therapy with the synthetic glucocorticoid (GC) methylprednisolone (MP). As most DMTs are not approved for use during pregnancy, treatment is usually discontinued, increasing the risk for relapses. While MP therapy during pregnancy is considered relatively save for the foetus, it may be detrimental for later cognitive and neuropsychiatric function. The underlying mechanism is thought to be an epigenetically mediated desensitisation of GC receptors, the subsequent increase in stress sensitivity, and a GC-mediated impairment of brain development. The aim of this study is to investigate the associations of foetal MP exposure in the context of MS relapse therapy with later cognitive function, brain development, stress sensitivity, and behaviour.

Methods and analysis

80 children aged 8 to 18 years of mothers with MS will be recruited. 40 children, exposed to GC in utero will be compared to 40 children without foetal GC exposure. The intelligence quotient will serve as primary outcome. Secondary outcomes will include attention, motor development, emotional excitability, Attention-Deficit Hyperactivity Disorder-related symptoms, and behavioural difficulties. The Trier Social Stress Test will test stress sensitivity, EEG and MRI will assess functional and structural brain development. To determine underlying mechanisms, DNA methylation of the GC receptor gene and the H19/IGF2 locus and changes in the microbiome and the metabolome will be investigated. Primary and secondary outcomes will be analysed using linear regression models. Time-variant outcomes of the stress test will be analysed in two mixed linear models exploring overall activity and change from baseline.

Ethics and dissemination

This study was approved by the participating institutions’ ethics committees and results will be presented in accordance with the STROBE 2007 Statement.

Trial registration

https://clinicaltrials.gov/ct2/show/NCT04832269?id=ZKSJ0130
Bayesian Logical Neural Networks for Human-Centered Applications in Medicine
Authors: Diaz O. Juan G. , Maier Lukas , Csiszár Orsolya
Published: November 2021

Medicine is characterized by its inherent ambiguity, i.e., the difficulty to identify and obtain exact outcomes from available data. Regarding this problem, electronic Health Records (EHRs) aim to avoid imprecisions in the data recording, for instance by its recording in an automatic way or by the integration of data that is both readable by humans and machines. However, the inherent biology and physiological processes introduce a constant epistemic uncertainty, which has a deep implication in the way the condition of the patients is estimated. For instance, for some patients, it is not possible to speak about an exact diagnosis, but about the “suspicion” of a disease, which reveals that the medical practice is often ambiguous. In this work, we report a novel modeling methodology combining explainable models, defined on Logic Neural Networks (LONNs), and Bayesian Networks (BN) that deliver ambiguous outcomes, for instance, medical procedures (Therapy Keys (TK)), depending on the uncertainty of observed data. If epistemic uncertainty is generated from the underlying physiology, the model delivers exact or ambiguous results depending on the individual parameters of each patient. Thus, our model does not aim to assist the customer by providing exact results but is a user-centered solution that informs the customer when a given recommendation, in this case, a therapy, is uncertain and must be carefully evaluated by the customer, implying that the final customer must be a professional who will not fully rely on automatic recommendations. This novel methodology has been tested on a database for patients with heart insufficiency.
Memory perfectionism is associated with persistent memory complaints after concussion
Authors: Picon Edwina L. , Todorova Evgenia , Palombo Daniela J. , Perez David L. , Howard Andrew , Silverberg Noah D.
Published: November 2021

Objective

The etiology of persistent memory complaints after concussion is poorly understood. Memory perfectionism (highly valuing memory ability and intolerance of minor memory lapses) may help explain why some people report persistent subjective memory problems in the absence of corresponding objective memory impairment. The present study investigated the relationship between memory perfectionism and persistent memory complaints after concussion.

Methods

Adults (N=77; 61% women) with persistent symptoms following concussion were recruited from outpatient specialty clinics. Participants completed the National Institutes of Health Toolbox Cognition Battery, Test of Memory Malingering-Trial 1, and questionnaires measuring memory perfectionism (Memory in Adulthood-Achievement subscale), forgetfulness and other post-concussion symptoms (Rivermead Postconcussion Symptoms Questionnaire; RPQ), and depression (Patient Health Questionnaire-2) at M=17.8 weeks post-injury. Patients with vs. without severe memory complaints (based on the RPQ) were compared.

Results

Memory perfectionism was associated with severe memory complaint, after controlling for objective memory ability, overall cognitive ability, and depression (95% confidence interval for odds ratio = 1.11 to 1.40). Sensitivity analyses showed that this relationship did not depend on use of specific objective memory tests nor on inclusion of participants who failed performance validity testing. In a control comparison to test the specificity of identified relationships, memory perfectionism was not associated with severe fatigue (95% confidence interval for odds ratio = 0.91 to 1.07).

Discussion

Memory perfectionism may predispose people to experience persistent memory symptoms and/or contribute to their perpetuation after concussion, with potential relevance to the spectrum of functional cognitive disorders more broadly.
Antibiotic resistance profile of E. coli isolates in 17 municipal wastewater utilities across Oregon
Authors: Khorshidi-Zadeh Marjan , Yiu Sue Yee , Nguyen Jacquelynn N. , Garza Gabriela L. , Waite-Cusic Joy , Radniecki Tyler S. , Navab-Daneshmand Tala
Published: November 2021

Wastewater treatment utilities are considered one of the main sources and reservoirs of antimicrobial resistance. The objective of this study was to determine the diversity and prevalence of antibiotic-resistant Escherichia coli in wastewater treatment systems across the state of Oregon. Influent, secondary effluent, final effluent, and biosolids were collected from 17 wastewater treatment utilities across Oregon during the winter and summer seasons of 2019 and 2020 (n = 246). E. coli strains were recovered from samples by culturing on mTEC, followed by confirmation with MacConkey with MUG agar plates. Antibiotic susceptibility of 1143 E. coli isolates against 8 antibiotics were determined, and resistance profiles and indices were analyzed between utilities, seasons, and flows. Antibiotic resistance phenotypes were detected in 31.6% of the collected E. coli isolates. Among those antibiotic-resistant E. coli isolates, multi-drug resistance (i.e., resistance to three or more classes of antibiotics) was harbored by 27.7% with some strains showing resistance to up to six classes of antibiotics. The most prevalent resistance was to ampicillin (n = 207) and the most common combinations of multi-drug resistance included simultaneous resistances to ampicillin, streptomycin, and tetracycline (n = 49), followed by ampicillin, streptomycin, and sulfamethoxazole/trimethoprim (n = 46). Significant correlations were observed between resistance to sulfamethoxazole/trimethoprim and resistances to ampicillin, ciprofloxacin, and tetracycline (p < 0.001). A small percentage (1.1%) of the E. coli isolates displayed extended-spectrum beta lactamase (ESBL) activity and a single isolate carried resistance to imipenem. Compared to wastewater influent, ciprofloxacin resistance was significantly more prevalent in biosolids (p <0.05) and tetracycline resistance was significantly lower in effluent (p <0.05). Seasonal impact on antibiotic-resistant E. coli in wastewater influent was observed through significantly higher multiple antibiotic resistance (MAR) index, ampicillin resistance prevalence, and ciprofloxacin resistance prevalence in summer compared to winter (p < 0.05). This state-wide study confirms the widespread distribution of antibiotic-resistant, multi-drug resistant, and extended-spectrum beta lactamase-producing E. coli in wastewater systems across different flows and seasonal variations, making them the recipients, reservoirs, and sources of antimicrobial resistance.
Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan function for the Hippo pathway in multicellular morphogenesis
Authors: Phillips Jonathan E , Santos Maribel , Kanchwala Mohammed , Xing Chao , Pan Duojia
Published: November 2021

Animal development is mediated by a surprisingly small set of canonical signaling pathways such as Wnt, Hedgehog, TGF-beta, Notch and Hippo pathways. Although once thought to be present only in animals, recent genome sequencing has revealed components of these pathways in the closest unicellular relatives of animals. These findings raise questions about the ancestral functions of these developmental pathways and their potential role in the emergence of animal multicellularity. Here, we provide the first functional characterization of any of these developmental pathways in unicellular organisms by developing techniques for genetic manipulation in Capsaspora owczarzaki, a close unicellular relative of animals that displays aggregative multicellularity. We then use these tools to characterize the Capsaspora ortholog of the Hippo signaling nuclear effector YAP/TAZ/Yorkie (coYki), a key regulator of tissue size in animals. In contrast to what might be expected based on studies in animals, we show that coYki is dispensable for cell proliferation but regulates cytoskeletal dynamics and the three-dimensional (3D) shape of multicellular structures. We further demonstrate that the cytoskeletal abnormalities of individual coYki mutant cells underlie the abnormal 3D shape of coYki mutant aggregates. Taken together, these findings implicate an ancestral role for the Hippo pathway in cytoskeletal dynamics and multicellular morphogenesis predating the origin of animal multicellularity, which was co-opted during evolution to regulate cell proliferation.
Explainability methods for differential gene analysis of single cell RNA-seq clustering models
Authors: Ciortan Madalina , Defrance Matthieu
Published: November 2021

Single-cell RNA sequencing (scRNA-seq) produces transcriptomic profiling for individual cells. Due to the lack of cell-class annotations, scRNA-seq is routinely analyzed with unsupervised clustering methods. Because these methods are typically limited to producing clustering predictions (that is, assignment of cells to clusters of similar cells), numerous model agnostic differential expression (DE) libraries have been proposed to identify the genes expressed differently in the detected clusters, as needed in the downstream analysis. In parallel, the advancements in neural networks (NN) brought several model-specific explainability methods to identify salient features based on gradients, eliminating the need for external models.

We propose a comprehensive study to compare the performance of dedicated DE methods, with that of explainability methods typically used in machine learning, both model agnostic (such as SHAP, permutation importance) and model-specific (such as NN gradient-based methods). The DE analysis is performed on the results of 3 state-of-the-art clustering methods based on NNs. Our results on 36 simulated datasets indicate that all analyzed DE methods have limited agreement between them and with ground-truth genes. The gradients method outperforms the traditional DE methods, which en-courages the development of NN-based clustering methods to provide an out-of-the-box DE capability. Employing DE methods on the input data preprocessed by clustering method outperforms the traditional approach of using the original count data, albeit still performing worse than gradient-based methods.
Cryptococcus neoformans capsule regrowth experiments reveal dynamics of enlargement and architecture
Authors: Wear Maggie P. , Jacobs Ella , Wang Siqing , McConnell Scott , Bowen Anthony , Strother Camilla , Cordero Radames J.B. , Casadevall Arturo
Published: November 2021

The polysaccharide capsule of fungal pathogen Cryptococcus neoformans is a critical virulence factor that has historically evaded characterization. Polysaccharides remain attached to the cell as capsular polysaccharide (CPS) or are shed into the surroundings in the form of exopolysaccharide (EPS). While a great deal of study has been done examining the properties of EPS, far less is known about CPS. In this work, we detail the development of new physical and enzymatic methods for the isolation of CPS which can be used to explore the architecture of the capsule and removed capsular material. Sonication and glucanex digestion yield soluble CPS preparations, while French Press and modified glucanex digestion plus vortexing remove the capsule and cell wall producing polysaccharide aggregates that we call ‘capsule ghosts.’ The existence of capsule ghosts implies an inherent organization that allows it to exist independent of the cell wall surface. As sonication and glucanex digestion were noncytotoxic, it was possible to observe the cryptococcal cells rebuilding their capsule, revealing new insights into capsule architecture and synthesis consistent with a model in which the capsule is assembled from smaller polymers, which are then assemble into larger ones.

Importance

Characterization of the cryptococcal polysaccharide capsule relies on methods of isolation for its in vitro study. This study demonstrates that the capsule is susceptible to physical and enzymatic removal. The application of new methods yields insights into the anatomy, modular nature, and architecture of the capsule with both soluble CPS preparations and ‘capsule ghosts.’ Together these insights inform on a long-standing debate modeling capsular assembly wherein our data shows that the capsule is assembled by smaller polymers added distally rather than by proximal addition or by polymers spanning the entire capsule radius.
Function of FMRP domains in regulating distinct roles of neuronal protein synthesis
Authors: D’Souza Michelle Ninochka , Ramakrishna Sarayu , Radhakrishna Bindushree K , Jhaveri Vishwaja , Ravindran Sreenath , Yeramala Lahari , Palakodeti Dasaradhi , Muddashetty Ravi S
Published: November 2021

The Fragile X Mental Retardation Protein (FMRP) is an RNA Binding Protein that regulates translation of mRNAs, essential for synaptic development and plasticity. FMRP interacts with a specific set of mRNAs and aids in their microtubule dependent transport and regulates their translation through its association with ribosomes. However, the biochemical role of individual domains of FMRP in forming neuronal granules and associating with microtubules and ribosomes is currently undefined. Here, we report that the C-terminus domain of FMRP is sufficient to bind to ribosomes as well as polysomes akin to the full-length protein. Furthermore, the C-terminus domain alone is essential and responsible for FMRP-mediated translation repression in neurons. However, FMRP-mediated puncta formation and microtubule association is favored by the synergistic combination of FMRP domains and not by individual domains. Interestingly, we show that the phosphorylation of hFMRP at Serine-500 is important in modulating the dynamics of translation by controlling ribosome/polysome association. This is a fundamental mechanism governing the size and number of FMRP puncta, which appear to contain actively translating ribosomes. Finally through the use of pathogenic mutations, we emphasize the hierarchy of the domains of FMRP in their contribution to translation regulation.
Activation of NLRP3 Inflammasome by Virus-like Particles of Human Polyomaviruses in Macrophages
Authors: Lučiūnaitė Asta , Dalgėdienė Indrė , Žilionis Rapolas , Mašalaitė Kristina , Norkienė Milda , Šinkūnas Andrius , Gedvilaitė Alma , Kučinskaitė-Kodzė Indrė , Žvirblienė Aurelija
Published: November 2021

Viral antigens can activate phagocytes inducing inflammation but the mechanisms are barely explored. This study aimed to investigate the capability of viral oligomeric proteins of different structure to induce inflammatory response in macrophages. Human THP-1 cell line was used to prepare macrophages which were treated with filamentous nucleocapsid-like particles (NLPs) of paramyxoviruses and spherical virus-like particles (VLPs) of human polyomaviruses. The effects of viral proteins on cell viability, pro-inflammatory cytokines’ production and formation of NLRP3 inflammasome components, ASC specks, were investigated. Filamentous NLPs did not induce inflammation markers while spherical VLPs mediated inflammatory response followed by NLRP3 inflammasome activation. Inhibitors of cathepsins and K+efflux decreased IL-1β levels and cell death indicating a complex inflammasome activation process. Similar activation pattern was observed in primary human macrophages treated with VLPs. Single cell RNAseq analysis of THP-1 cells revealed several cell activation states characterized by high expression of inflammation-related genes. This study provides new insights into interaction of viral proteins with innate immune cells and suggests that structural properties of oligomeric proteins may define cell activation pathways.
Predicting human decision making in psychological tasks with recurrent neural networks
Authors: Lin Baihan , Bouneffouf Djallel , Cecchi Guillermo
Published: November 2021

Unlike traditional time series, the action sequences of human decision making usually involve many cognitive processes such as beliefs, desires, intentions and theory of mind, i.e. what others are thinking. This makes predicting human decision making challenging to be treated agnostically to the underlying psychological mechanisms. We propose to use a recurrent neural network architecture based on long short-term memory networks (LSTM) to predict the time series of the actions taken by the human subjects at each step of their decision making, the first application of such methods in this research domain. In this study, we collate the human data from 8 published literature of the Iterated Prisoner’s Dilemma comprising 168,386 individual decisions and postprocess them into 8,257 behavioral trajectories of 9 actions each for both players. Similarly, we collate 617 trajectories of 95 actions from 10 different published studies of Iowa Gambling Task experiments with healthy human subjects. We train our prediction networks on the behavioral data from these published psychological experiments of human decision making, and demonstrate a clear advantage over the state-of-the-art methods in predicting human decision making trajectories in both single-agent scenarios such as the Iowa Gambling Task and multi-agent scenarios such as the Iterated Prisoner’s Dilemma. In the prediction, we observe that the weights of the top performers tends to have a wider distribution, and a bigger bias in the LSTM networks, which suggests possible interpretations for the distribution of strategies adopted by each group.

Author summary

The challenge of predicting human decision is important for many application domains like economy, marketing and artificial intelligence. But the domain where the human behavior modeling is especially crucial is psychology, where the goal is to describe, explain and predict these behaviors. Within this domain, creating agents that effectively mimic human decision making is particularly important. However, despite the many behavioral tasks and analytical methods developed to simulate the process of human decision making in real situations, there have not been a predictive model that can well predict the human decision making trajectories in these psychological tasks. In this predictive modeling problem, we propose to use the long short-term memory networks (LSTM), a popular recurrent neural network architecture and effectively predict the time series of the actions taken by the human subjects at each step of their decision making in both the Iowa Gambling Task, a single-agent game with monetary reward, and the Iterated Prisoner’s Dilemma, a complex multi-agent social game with non-monetary capital at stake. To the best of our knowledge, this is the first application of such methods in this research domain.
Improved two-photon imaging of GPCR-based optogenetic neurotransmitter sensors using orthogonally polarized excitation
Authors: Pulin Mauro , Stockhausen Kilian E. , Masseck Olivia Andrea , Kubitschke Martin , Busse Björn , Wiegert J. Simon , Oertner Thomas G.
Published: November 2021

Fluorescent proteins such as GFP are best excited by light that is polarized parallel to the dipole axis of the fluorophore. In most cases, fluorescent proteins are randomly oriented, resulting in unbiased images even when polarized light is used for excitation, e.g. in two-photon microcopy. Here we reveal a surprisingly strong polarization sensitivity in a class of GPCR-based neurotransmitter sensors where the fluorophore is anchored on both ends. In tubular structures such as dendrites, this effect led to a complete loss of membrane signal in dendrites running parallel to the polarization direction of the excitation beam. Our data reveal a major problem for two-photon measurements of neurotransmitter concentration that has not been recognized by the neuroscience community. To remedy the sensitivity to dendritic orientation, we designed an optical device that generates interleaved pulse trains of orthogonal polarization, removing the orientation bias from images. The passive device, which we inserted in the beam path of an existing two-photon microscope, also removed the strong direction bias in second harmonic generation (SHG) images. We conclude that for optical measurements of transmitter concentration with GPCR-based sensors, orthogonally polarized excitation is essential.
Influence of the extracellular domain size on the dynamic behavior of membrane proteins
Authors: Gurdap Cenk Onur , Wedemann Linda , Sych Taras , Sezgin Erdinc
Published: November 2021

The dynamic behavior of plasma membrane proteins mediates various cellular processes such as cellular motility, communication, and signaling. It is widely accepted that the dynamics of the membrane proteins is determined either by the interactions of the transmembrane domain with the surrounding lipids or by the interactions of the intracellular domain with cytosolic components such as cortical actin. Although initiation of different cellular signaling events at the plasma membrane has been attributed to the extracellular domain (ECD) properties recently, the impact of ECDs on the dynamic behavior of membrane proteins is rather unexplored. Here, we investigate how the ECD properties influence protein dynamics in the lipid bilayer by reconstituting ECDs of different sizes or glycosylation in model membrane systems and analyzing ECD-driven protein sorting in lipid domains as well as protein mobility. Our data shows that increasing the ECD mass or glycosylation leads to a decrease in ordered domain partitioning and diffusivity. Our data reconciles different mechanisms proposed for the initiation of cellular signaling by linking the ECD size of membrane proteins with their localization and diffusion dynamics in the plasma membrane.

SIGNIFICANCE STATEMENT

We studied how the size and glycosylation of the proteins influences their dynamic behavior in a lipid bilayer by reconstituting the ECDs of different sizes or glycosylation in model membrane systems and analyzing their sorting into lipid domains as well as their mobility. We observe that increasing the ECD apparent mass leads to a decrease in membrane ordered domain partitioning and diffusivity. Our data reconciles multiple mechanisms proposed for the initiation of cellular signaling by linking the ECD properties of membrane proteins with their localization and diffusion dynamics in the plasma membrane.
Mobilome-driven segregation of the resistome in biological wastewater treatment
Authors: de Nies Laura , Busi Susheel Bhanu , Kunath Benoit Josef , May Patrick , Wilmes Paul
Published: November 2021

Biological wastewater treatment plants (BWWTP) are considered to be hotspots of evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of fifteen AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS, sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both MGEs. Subsequent expression- and protein-level analyses further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. Longitudinal assessment further underlined these findings whereby the log2-fold changes of aminoglycoside, bacitracin and sulfonamide resistance genes were increased in plasmids, while fosfomycin and peptide resistance showed similar trends in phages. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, for which MGEs also contributed differentially to the dissemination of ARGs. Collectively our findings pave the way towards understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.
Niche differences, not fitness differences, explain coexistence across ecological groups
Authors: Buche Lisa , Spaak Jurg W. , Jarillo Javier , De Laender Frederik
Published: November 2021

Understanding the drivers of species coexistence is an important objective in ecology. Yet, the multitude of methods to study coexistence hampers cross-community comparisons. Here, we standardized niche and fitness differences (i.e how species limit themselves compared to others and their competitive ability, respectively) across 1018 species pairs to investigate species coexistence across ecological groups and methodological settings (experimental setup, natural co-occurrence, population model used, and growth method). We find that, first, coexistence is driven by large niche differences, not by small fitness differences. Second, species group into clear clusters of coexisting and non-coexisting species along the niche axis. Finally, these clusters are not driven by ecological or methodological settings. This suggests differences between coexisting and non-coexisting communities transcending those measured in our empirical systems. Overall, our results show that species coexistence is mainly influenced by mechanisms acting on niche differences.
A general design of caging-group free photoactivatable fluorophores for live-cell nanoscopy
Authors: Lincoln Richard , Bossi Mariano L. , Remmel Michael , D’Este Elisa , Butkevich Alexey N. , Hell Stefan W.
Published: November 2021

The controlled switching of fluorophores between non-fluorescent and fluorescent states is central to every superresolution fluorescence microscopy (nanoscopy) technique, and the exploration of radically new switching mechanisms remains critical to boosting the performance of established, as well as emerging superresolution methods. Photoactivatable dyes offer significant improvements to many of these techniques, but often rely on photolabile protecting groups that limit their applications. Here we describe a general method to transform 3,6-diaminoxanthones into caging-group free photoactivatable fluorophores. These photoactivatable xanthones (PaX) assemble rapidly and cleanly into highly fluorescent, photo- and chemically stable pyronine dyes upon irradiation with light. The strategy is extendable to carbon- and silicon-bridged xanthone analogs, yielding a new family of photoactivatable labels spanning much of the visible spectrum. Our results demonstrate the versatility and utility of PaX dyes in fixed and live-cell fluorescence microscopy, and both coordinate-targeted stimulated emission depletion (STED) and coordinate-stochastic single-molecule localization superresolution microscopy (SMLM).
Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder
Authors: Fuentes-Cabrera Miguel , Sakkos Jonathan K. , Ducat Daniel C. , Ziatdinov Maxim
Published: November 2021

Carboxysomes are a class of bacterial microcompartments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive toCO2fixation. Critical aspects of the assembly of the carboxysomes remain relatively unknown, especially with regard to the dynamics of this microcompartment. We have recently expressed an exogenous protease as a way of gaining control over endogenous protein levels, including carboxysomal components, in the model cyanobacteriumSynechococcous elongatusPCC 7942. By utilizing this system, proteins that compose the carboxysome can be tuned in real-time as a method to examine carboxysome dynamics. Yet, analysis of subtle changes in carboxysome morphology with microscopy remains a low-throughput and subjective process. Here we use deep learning techniques, specifically a Rotationally Invariant Variational Autoencoder (rVAE), to analyze the fluorescence microscopy images and quantitatively evaluate how carboxysome shell remodelling impacts trends in the morphology of the microcompartment over time. We find that rVAEs are able to assist in the quantitative evaluation of changes in carboxysome location, shape, and size over time. We propose that rVAEs may be a useful tool to accelerate the analysis of carboxysome assembly and dynamics in response to genetic or environmental perturbation, and may be more generally useful to probe regulatory processes involving a broader array of bacterial microcompartments.
Engraftment of allotransplantated tumour cells in adult rag2 mutant Xenopus tropicalis
Authors: Tulkens Dieter , Dimitrakopoulou Dionysia , Van Nieuwenhuysen Tom , Boelens Marthe , Demuynck Suzan , Toussaint Wendy , Creytens David , Van Vlierberghe Pieter , Vleminckx Kris
Published: November 2021

Modelling human genetic diseases and cancer in lab animals has been greatly aided by the emergence of genetic engineering tools such as TALENs and CRISPR/Cas9. We have previously demonstrated the ease with which genetically engineered Xenopus models (GEXM) can be generated. This included the induction of autochthonous tumour formation by injection of early embryos with Cas9 recombinant protein loaded with sgRNAs targeting multiple tumour suppressor genes. What has been lacking so far is the possibility to propagate the induced cancers via transplantation. In this paper we describe the generation of a rag2-/- knock-out line in Xenopus tropicalis that is deficient in functional T- and B-cells. This line was validated by means of an allografting experiment with a primary tp53-/- donor tumour. In addition, we optimized available protocols for sub-lethal gamma irradiation of X. tropicalis froglets. Irradiated animals also allowed stable, albeit transient, engraftment of transplanted tp53-/- tumour cells. The novel X. tropicalis rag2-/- line and the irradiated wild type froglets will further expand the experimental toolbox in this diploid amphibian, and help to establish it as a versatile and relevant model for exploring human cancer.
Effector loss drives adaptation of Pseudomonas syringae pv. actinidiae to Actinidia arguta
Authors: Hemara Lauren M. , Jayaraman Jay , Sutherland Paul W. , Montefiori Mirco , Arshed Saadiah , Chatterjee Abhishek , Chen Ronan , Andersen Mark , Mesarich Carl H. , van der Linden Otto , Schipper Magan M. , Vanneste Joel L. , Brendolise Cyril , Templeton Matthew D.
Published: November 2021

A pandemic isolate ofPseudomonas syringaepv.actinidiaebiovar 3 (Psa3) has devastated kiwifruit orchards growing cultivars ofActinidia chinensis. In contrast,A. arguta(kiwiberry) is resistant to Psa3. This resistance is mediated via effector-triggered immunity, as demonstrated by induction of the hypersensitive response in infectedA. argutaleaves, observed by microscopy and quantified by ion-leakage assays. Isolates of Psa3 that cause disease inA. argutahave been isolated and analyzed, revealing a 49 kb deletion in the exchangeable effector locus (EEL). This natural EEL-mutant isolate and strains with synthetic knockouts of the EEL were more virulent inA. argutaplantlets than wild-type Psa3. Screening of a complete library of Psa3 effector knockout strains identified increased growthin plantafor knockouts of four effectors – AvrRpm1a, HopF1c, HopZ5a, and the EEL effector HopAW1a – suggesting a resistance response inA. arguta. Hypersensitive response (HR) assays indicate that three of these effectors trigger a host species-specific HR. A Psa3 strain with all four effectors knocked out escaped host recognition, but a cumulative increase in bacterial pathogenicity and virulence was not observed. These avirulence effectors can be used in turn to identify the first cognate resistance genes inActinidiafor breeding durable resistance into future kiwifruit cultivars.
Experience with open schools and preschools in periods of high community transmission of COVID-19 in Norway during the academic year of 2020/2021
Authors: Stebbings Sara , Rotevatn Torill Alise , Larsen Vilde Bergstad , Surén Pål , Elstrøm Petter , Greve-Isdahl Margrethe , Johansen Tone Bjordal , Astrup Elisabeth
Published: November 2021

Background

Schools and preschools have largely remained open in Norway throughout the pandemic, with flexible mitigation measures in place. This contrasts with many other high-income countries that closed schools for long periods of time. Here we describe cases and outbreaks of COVID-19 in schools and preschools during the academic year 2020/2021, to evaluate the strategy of keeping these open with infection prevention control measures in place.

Methods

In this descriptive study, the Norwegian Institute of Public Health initiated systematic surveillance for COVID-19 cases and outbreaks in schools and preschools in October 2020. Data was compiled from the national outbreak alert system VESUV, municipality websites, and media scanning combined with the national emergency preparedness register Beredt C-19. An outbreak was defined as ≥ 2 cases among pupils or staff within 14 days at the same educational setting. Settings were categorized as preschool (1-5-years), primary school (6-12-years), lower secondary school (13-15-years) and upper secondary school (16-18-years). We reported the incidence rate among preschool and school-aged pupils and gave a descriptive overview of outbreaks and included cases per educational setting.

Results

During the whole academic year, a total of 1203 outbreaks in preschools and school settings were identified, out of a total of 8311 preschools and schools nationwide. The incidence of COVID-19 in preschool- and school-aged children and the rates of outbreaks in these settings largely followed the community trend. Most of the outbreaks occurred in primary schools (40%) and preschools (25%). Outbreaks across all settings were mostly small (median 3 cases, range 2 to 72), however, 40 outbreaks (3% of total) included 20 or more cases. The larger outbreaks were predominantly seen in primary schools (43%).

Conclusions

We observed few large outbreaks in open schools and preschools in Norway during the academic year of 2020/2021, also when the Alpha variant was predominant. This illustrates that it is possible to keep schools and preschools open even during periods of high community transmission of COVID-19. Adherence to targeted IPC measures adaptable to the local situation has been essential to keep educational settings open, and thus reduce the total burden on children and adolescents.
Developing a taxonomy of care coordination for people living with rare conditions: A qualitative study
Authors: Walton Holly , Simpson Amy , Ramsay Angus I.G. , Hudson Emma , Hunter Amy , Jones Jennifer , Li Ng Pei , Leeson-Beevers Kerry , Bloom Lara , Kai Joe , Kerecuk Larissa , Kokocinska Maria , Sutcliffe Alastair G , Morris Stephen , Fulop Naomi J
Published: November 2021

Background

Improving care coordination is particularly important for individuals with rare conditions (who may experience multiple inputs into their care, across different providers and settings). To develop and evaluate strategies to potentially improve care coordination, it is necessary to develop a method for organising different ways of coordinating care for rare conditions. Developing a taxonomy would help to describe different ways of coordinating care and in turn facilitate development and evaluation of pre-existing and new models of care coordination for rare conditions. To the authors’ knowledge, no studies have previously developed taxonomies of care coordination for rare conditions. This research aimed to develop and refine a care coordination taxonomy for people with rare conditions.

Methods

This study had a qualitative design and was conducted in the United Kingdom. To develop a taxonomy, six stages of taxonomy development were followed. We conducted interviews (n=30 health care professionals/charity representatives/commissioners) and focus groups (n=4 focus groups, 22 patients/carers with rare/ultra-rare/undiagnosed conditions). Interviews and focus groups were audio-recorded with consent, and professionally transcribed. Findings were analysed using thematic analysis. Themes were used to develop a taxonomy, and to identify which types of coordination may work best in which situations. To refine the taxonomy, we conducted two workshops (n=12 patients and carers group; n=15 professional stakeholder group).

Results

Our taxonomy has six domains, each with different options. The six domains are: 1) Ways of organising care (local, hybrid, national), 2) Ways of organising professionals involved in care (collaboration between many or all professionals, collaboration between some professionals, a lack of collaborative approach), 3) Responsibility for coordination (administrative support, formal roles and responsibilities, supportive roles and no responsibility), 4) How often appointments and coordination take place (regular, on demand, hybrid), 5) Access to records (full or filtered access), and 6) Mode of care coordination (face-to-face, digital, telephone).

Conclusions

Findings indicate that there are different ways of coordinating care across the six domains outlined in our taxonomy. This may help to facilitate the development and evaluation of existing and new models of care coordination for people living with rare conditions.
Fisher information for optimal planning of X-ray diffraction experiments
Authors: Mikhalychev Alexander , Zhevno Konstantin , Vlasenko Svetlana , Benediktovitch Andrei , Ulyanenkova Tatjana , Ulyanenkov Alex
Published: November 2021

Fisher information is a powerful mathematical tool suitable for quantification of data `informativity' and optimization of the experimental setup and measurement conditions. Here, it is applied to X-ray diffraction and an informational approach to choosing the optimal measurement configuration is proposed. The core idea is maximization of the information which can be extracted from the measured data set by the selected analysis technique, over the sets of accessible reflections and measurement geometries. The developed approach is applied to high-resolution X-ray diffraction measurements and microstructure analysis of multilayer samples, and its efficiency and consistency are demonstrated with the results of more straightforward Monte Carlo simulations.
In situsmall-angle X-ray scattering investigation of X-ray-induced gold nanoparticle synthesis without stabilizer
Authors: Li Fangzuo , Xu Qianqian , Xia Wenjing , Zhang Xiang , Zhao Weidong , Zhou Lili , Zhong Haijian , Peng Weijie , Liu Zhiguo , Sun Tianxi
Published: November 2021

The X-ray irradiation of gold salt aqueous solutions in the synthesis of gold nanoparticles (AuNPs) in the absence of any reducing agent or stabilizer is presented. The size, dispersion, number of particles, yield and morphology evolution during the radiolytic formation of AuNPs were followed simultaneously usingin situsmall-angle X-ray scattering. This study provides an insight into the overall kinetics and formation mechanisms at the initial stage of AuNP synthesis without reductants and stabilizers. The pH-dependent speciation of aqueous HAuCl4and its influence on the synthesis, structure and properties of AuNPs were observed. The result sheds light on the key parameters required to obtain stable monomodal particles and the influence of the surface charge and reactivity of the chemical solution on the final particle size and shape.
Growing a thriving international community for small-angle scattering through collaboration. Corrigendum
Authors: Trewhella Jill
Published: November 2021

Errors in the article by Jill Trewhella [J. Appl. Cryst. (2021), 54, 1029–1033] are corrected.