bluuebunny/crossref_metadata_2025 huggingface dataset:
The implications of religious event and holidays on the transmission of SARS-CoV2 : the impact of behavioral changes on transmission
Authors: Abdulrahman Abdulkarim , AlMajthoob Muath , AlAwadhi Abdulla I , AlQahtani Manaf M
Published: October 2020

Introduction

The risk factors for transmission of SARS-CoV2 have been widely studied and it was evident that a population’s behavior has a direct effect on the risk of transmission. Public health measures and regulation are largely kept to control and direct these behaviors. In this study, we describe the change in transmission in SARS-CoV2 in relation to demographics before and after two major religious events: “Eid Alfitr” and “Ashura”

Methods

This is a national observational study conducted in Bahrain in September 2020 to compare the number and demographics of all newly diagnosed cases before and after Eid Alfitr (religious holiday) and Ashura religious event. A 10 day period before the event was compared to a 10 day period after the event by ten days. Data on the number of tests, number of new cases, their demographics (age, gender, nationality) and presence of symptoms were collected and analyzed.

Results

There was significant increase in the number of COVID-19 cases after both Eid Alfitr (1997 more cases, with a 67% increase) and Ashura (4232 more cases with 2.19 times more cases). The majority of new cases after the religious events were found in local Bahrainis, from 472 cases to 2169 cases after Eid, and from 2201 to 6639 cases after Ashura. The rise was most notable in females (increased by 4.89 times after Eid and by 2.69 times after Ashura), children (increased by 4.69 times after Eid and by 5 times after Ashura) and elderly above the age of 60 years (increased by 5.7 times after Eid and by 3.23 times after Ashura).

Conclusion

It is evident that religious events and holidays have important implications on the transmission of SARS-CoV2. This increased in transmission is related mainly to the behavior of the population in those days. Children, female, and elderly were the most affected categories due to these events. A thorough public health plan to limit the spread of the infection at these events should be planned and implemented ahead of time.
Real-time tracking and prediction of COVID-19 infection using digital proxies of population mobility and mixing
Authors: Leung Kathy , Wu Joseph T , Leung Gabriel M
Published: October 2020

Digital proxies of human mobility and physical mixing have been used to monitor viral transmissibility and effectiveness of social distancing interventions in the ongoing COVID-19 pandemic. We developed a new framework that parameterizes disease transmission models with age-specific digital mobility data. By fitting the model to case data in Hong Kong, we were able to accurately track the local effective reproduction number of COVID-19 in near real time (i.e. no longer constrained by the delay of around 9 days between infection and reporting of cases) which is essential for quick assessment of the effectiveness of interventions on reducing transmissibility. Our findings showed that accurate nowcast and forecast of COVID-19 epidemics can be obtained by integrating valid digital proxies of physical mixing into conventional epidemic models.
Minimum Dietary Diversity and Associated Factors among Lactating Mothers in Ataye District, North Shoa Zone, Central Ethiopia: A Community-based Cross-sectional Study
Authors: Getacher Lemma , Egata Gudina , Alemayehu Tadesse , Bante Agegnehu , Molla Abebaw
Published: October 2020

Background

Low dietary diversity superimposed with poor quality monotonous diets is a major problem that often results in undernutrition, mainly micronutrient deficiencies. However, there is limited evidence on minimum dietary diversity and associated factors among lactating mothers in resource-poor settings, including the study area. Therefore, the objective of the study is to assess the prevalence of minimum dietary diversity and associated factors among lactating mothers in Ataye District, Ethiopia.

Methods

A community-based cross-sectional study design was used among 652 lactating mothers aged 15-49 years from January 25 to April 30, 2018. Dietary diversity was measured by the minimum dietary diversity indicator for women (MDD-W) using the 24-hour dietary recall method. Data were entered into EpiData version 4.2.0.0 and exported to the statistical package for social science (SPSS) version 24 for analysis using the logistic regression model.

Results

The prevalence of minimum dietary diversity among lactating mothers was 48.8%, (95% CI: (44.7%, 52.9%). Having formal education [(AOR=2.16, 95% CL: (1.14, 4.09)], a final say on household purchases [(AOR=5.39, 95% CI: (2.34, 12.42)], home gardening practices [(AOR=2.67, 95% CI: (1.49, 4.81)], a history of illness [(AOR=0.47, 95% CI: (0.26, 0.85), good knowledge of nutrition [(AOR=5.11, 95% CI: (2.68, 9.78)], being from food-secure households [(AOR=2.96, 95% CI: (1.45, 6.07)] and medium [(AOR=5.94, 95% CI: (2.82, 12.87)] and rich wealth indices [(AOR= 3.55, 95% CI: (1.76, 7.13)] were significantly associated with minimum dietary diversity.

Conclusion

The prevalence of minimum dietary diversity among lactating mothers was low in the study area. It was significantly associated with mothers having a formal education, final say on the household purchase, home garden, good knowledge of nutrition, history of illness, food-secure households and belonging to medium and rich household wealth indices. Therefore, efforts should be made to improve the mothers decision-making autonomy, nutrition knowledge, household food security and wealth status.
Temporal course of SARS-CoV-2 antibody positivity in patients with COVID-19 following the first clinical presentation
Authors: Risch Martin , Weber Myriam , Thiel Sarah , Grossmann Kirsten , Wohlwend Nadia , Lung Thomas , Hillmann Dorothea , Ritzler Michael , Ferrara Francesca , Bigler Susanna , Egli Konrad , Bodmer Thomas , Imperiali Mauro , Salimi Yacir , Fleisch Felix , Cusini Alexia , Renz Harald , Kohler Philipp , Vernazza Pietro , Kahlert Christian , Paprotny Matthias , Risch Lorenz
Published: October 2020

Knowledge of the sensitivities of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antibody tests beyond 35 days after the clinical onset of COVID-19 is insufficient. We aimed to describe positivity rate of SARS-CoV-2 assays employing three different measurement principles over a prolonged period. Two hundred sixty-eight samples from 180 symptomatic patients with COVID-19 and a reverse transcription polymerase chain reaction (RT-PCR) test followed by serological investigation of SARS-CoV-2 antibodies were included.. We conducted three chemiluminescence (including electrochemiluminscence, ECLIA), four enzyme linked immunosorbent assay (ELISA), and one lateral flow immunoassay (LFIA) test formats. Positivity rates, as well as positive (PPV) and negative predictive values (NPV) were calculated for each week after the first clinical presentation for COVID-19. Furthermore, combinations of tests were assessed within an orthogonal testing approach employing two independent assays and predictive values were calculated. Heat maps were constructed to graphically illustrate operational test characteristics. During a follow-up period of more than 9 weeks, chemiluminescence assays and one ELISA IgG test showed stable positivity rates after the third week. With the exception of ECLIA, the PPVs of the other chemiluminescence assays were ≥95% for COVID-19 only after the second week. ELISA and LFIA had somewhat lower PPVs. IgM exhibited insufficient predictive characteristics. An orthogonal testing approach provided PPVs ≥95% for patients with a moderate pretest probability (e.g., symptomatic patients), even for tests with a low single test performance. After the second week, NPVs of all but IgM assays were ≥95% for patients with low to moderate pretest probability. The confirmation of negative results using an orthogonal algorithm with another assay provided lower NPVs than the single assays. When interpreting results from SARS-CoV-2 tests, the pretest probability, time of blood draw and assay characteristics must be carefully considered. An orthogonal testing approach increases the accuracy of positive, but not negative, predictions.
Spatial modelling of sand fly vector’s response to a synthetic sex-aggregation pheromone: impact on the incidence of visceral leishmaniasis in rural and urban settings
Authors: Retkute Renata , Dilger Erin , Hamilton James GC , Keeling Matt J , Courtenay Orin
Published: October 2020

Background

Visceral leishmaniasis (VL) is a potentially fatal protozoan parasitic disease of humans and dogs. In the Americas, dogs are the reservoir and Lutzomyia longipalpis is the sand fly vector. A synthetic version of the vector’s sex-aggregation pheromone attracts conspecifics to co-located lethal insecticide, reducing reservoir infection and vector abundance. Mathematical models of spatially deployed interventions are lacking, thus best practise using this novel lure-and-kill vector control approach to reduce infection incidence has not been fully explored.

Methods

We developed a predictive mathematical model of vector host-seeking behaviour combined with spatially explicit transmission models to evaluate changes in human and canine spatial infection incidence under variable pheromone implementation scenarios and demographic conditions.

Results

The risk of human infection increased exponentially with canine incidence, but at different rates between rural and urban settings with spatial clustering of high forces of human infection related to their proximity to canine infected households. A predicted 70% household coverage using a cost-effective amount (50mg) of pheromone, plus insecticide, reduced rural and urban setting infection incidence by approximately 44% and 50% in dogs, and by 64% and 68% in humans, within 1-2 years. Near or complete transmission elimination in dogs and humans was achieved after 10 years intervention using 50mg of pheromone under 70% household coverage in urban settings when newly acquired (immigrant) dogs had no pre-existing infections, but in rural settings required 90% coverage using 500mg. The willingness to pay (WTP) price per 10mg unit of pheromone is likely to be <$3 USD, making it a cost-beneficial intervention compared to current alternative strategies.

Conclusions

Integrated stochastic and spatial models capturing vector host-seeking behaviour, is a useful mathematical framework to evaluate spatially dependent intervention methods, fine-scale transmission dynamics, and to identify best practise.
Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of Covid-19 in England
Authors: Sherratt Katharine , Abbott Sam , Meakin Sophie R , Hellewell Joel , Munday James D , Bosse Nikos ,   CMMID Covid-19 working group, Jit Mark , Funk Sebastian
Published: October 2020

The time-varying reproduction number (Rt: the average number secondary infections caused by each infected person) may be used to assess changes in transmission potential during an epidemic. While new infections are not usually observed directly, they can be estimated from data. However, data may be delayed and potentially biased. We investigated the sensitivity of Rt estimates to different data sources representing Covid-19 in England, and we explored how this sensitivity could track epidemic dynamics in population sub-groups.

We sourced public data on test-positive cases, hospital admissions, and deaths with confirmed Covid-19 in seven regions of England over March through August 2020. We estimated Rt using a model that mapped unobserved infections to each data source. We then compared differences in Rt with the demographic and social context of surveillance data over time.

Our estimates of transmission potential varied for each data source, with the relative inconsistency of estimates varying across regions and over time. Rt estimates based on hospital admissions and deaths were more spatio-temporally synchronous than when compared to estimates from all test-positives. We found these differences may be linked to biased representations of subpopulations in each data source. These included spatially clustered testing, and where outbreaks in hospitals, care homes, and young age groups reflected the link between age and severity of disease.

We highlight that policy makers could better target interventions by considering the source populations of Rt estimates. Further work should clarify the best way to combine and interpret Rt estimates from different data sources based on the desired use.
2008 financial crisis vs 2020 economic fallout: How COVID-19 might influence fertility treatment and live births
Authors: Gromski Piotr S. , Smith Andrew D.A.C , Lawlor Deborah A , Sharara Fady I. , Nelson Scott M
Published: October 2020

Background

The economic and reproductive medicine response to the COVID-19 pandemic in the United States has reduced the affordability and accessibility of fertility care. We sought to determine the impact of the 2008 financial recession and the COVID-19 recession on fertility treatments and cumulative live-births.

Methods

We examined annual US natality, CDC IVF cycle activity and live birth data from 1999 to 2018 encompassing 3,286,349 treatment cycles, to estimate the age-stratified reduction in IVF cycles undertaken after the 2008 financial recession, with forward quantitative modelling of IVF cycle activity and cumulative live-births for 2020 to 2023.

Results

The financial recession of 2008 caused a four-year plateau in fertility treatments with a predicted 53,026 (95% CI 49,581 to 56,471) fewer IVF cycles and 16,872 (95% CI 16,713 to 17,031) fewer live births. A similar scale of economic recession would cause 67,386 (95% CI: 61,686 to 73,086) fewer IVF cycles between 2020 and 2023, with women younger than 35 years overall undertaking 22,504 (95% CI 14,320 to 30,690) fewer cycles, as compared to 4,445 (95% CI 3,144 to 5749) fewer cycles in women over the age of 40 years. This equates to overall 25,143 (95% CI: 22,408 to 27,877) fewer predicted live-births from IVF, of which only 490 (95% CI 381 to 601) are anticipated to occur in women over the age of 40 years.

Conclusions

The COVID-19 recession could have a profound impact on US IVF live-birth rates in young women, further aggravating pre-existing declines in total fertility rates.

Trial registration number

not applicable
Supporting COVID-19 Policy-Making with a Predictive Epidemiological Multi-Model Warning System
Authors: Bicher Martin , Zuba Martin , Rainer Lukas , Bachner Florian , Rippinger Claire , Ostermann Herwig , Popper Nikolas , Thurner Stefan , Klimek Peter
Published: October 2020

In response to the SARS-CoV-2 pandemic, the Austrian governmental crisis unit commissioned a forecast consortium with regularly projections of case numbers and demand for hospital beds. The goal was to assess how likely Austrian ICUs would become overburdened with COVID-19 patients in the upcoming weeks. We consolidated the output of three independent epidemiological models (ranging from agent-based micro simulation to parsimonious compartmental models) and published weekly short-term forecasts for the number of confirmed cases as well as estimates and upper bounds for the required hospital beds. Here, we report on three key contributions by which our forecasting and reporting system has helped shaping Austria’s policy to navigate the crisis, namely (i) when and where case numbers and bed occupancy are expected to peak during multiple waves, (ii) whether to ease or strengthen non-pharmaceutical intervention in response to changing incidences, and (iii) how to provide hospital managers guidance to plan health-care capacities. Complex mathematical epidemiological models play an important role in guiding governmental responses during pandemic crises, in particular when they are used as a monitoring system to detect epidemiological change points.
Urine single cell RNA-sequencing in focal segmental glomerulosclerosis reveals inflammatory signatures in immune cells and podocytes
Authors: Latt Khun Zaw , Heymann Jurgen , Jessee Joseph H. , Rosenberg Avi Z. , Berthier Celine C. , Eddy Sean , Yoshida Teruhiko , Zhao Yongmei , Chen Vicky , Nelson George W. , Cam Margaret , Kumar Parimal , Mehta Monika , Kelly Michael C. , Kretzler Matthias ,   The Nephrotic Syndrome Study Network (NEPTUNE),   The Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) consortium, Cheryl, Winkler A. , Kopp Jeffrey B.
Published: October 2020

The diagnosis of focal segmental glomerulosclerosis (FSGS) requires a renal biopsy, which is invasive and can be problematic in children and in some adults. We used single cell RNA-sequencing to explore disease-related cellular signatures in 23 urine samples from 12 FSGS subjects. We identified immune cells, predominantly monocytes, and renal epithelial cells, including podocytes. Analysis revealed M1 and M2 monocyte subsets, and podocytes showing high expression of genes for epithelial-to-mesenchymal transition (EMT). We confirmed M1 and M2 gene signatures using published monocyte/macrophage data from lupus nephritis and cancer. Using renal transcriptomic data from the Nephrotic Syndrome Study Network (NEPTUNE), we found that urine cell immune and EMT signature genes showed higher expression in FSGS biopsies compared to minimal change disease biopsies. These results suggest that urine cell profiling may serve as a diagnostic and prognostic tool in nephrotic syndrome and aid in identifying novel biomarkers and developing personalized therapeutic strategies.
Alteration of coastal productivity and artisanal fisheries interact to affect a marine food-web
Authors: Ávila-Thieme M. Isidora , Corcoran Derek , Pérez-Matus Alejandro , Wieters Evie A. , Navarrete Sergio A. , Marquet Pablo A. , Valdovinos Fernanda S.
Published: October 2020

Top-down and bottom-up forces determine ecosystem function and dynamics. Fisheries as a top-down force can shorten and destabilize food-webs, while climate-change driven effects can alter the bottom-up forces of primary productivity. We assessed the response of a highly-resolved intertidal food-web to these two global-change drivers, using network analysis and bioenergetic modelling. We quantified the relative importance of artisanal fisheries as another predator species, and evaluated the independent and combined effects of fisheries and plankton-productivity changes on food-web dynamics. The food-web was robust to the loss of all harvested species but sensible to plankton-productivity decline. Interestingly, fisheries dampened the negative impacts of decreasing plankton productivity on non-harvested species, while plankton-productivity decline increased the sensitivity of harvested species to fishing. Our results show that strategies for new scenarios caused by climate change are needed to protect marine ecosystems and the wellbeing of local communities dependent on their resources.
An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
Authors: Chan Kui K. , Tan Timothy J.C. , Narayanan Krishna K. , Procko Erik
Published: October 2020

The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE22.v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
Multimodal Analysis for Human ex vivo Studies Shows Extensive Molecular Changes from Delays in Blood Processing
Authors: Savage Adam K. , Gutschow Miriam V. , Chiang Tony , Henderson Kathy , Green Richard , Chaudhari Monica , Swanson Elliott , Heubeck Alexander T. , Kondza Nina , Burley Kelli C. , Genge Palak C. , Lord Cara , Smith Tanja , Thomson Zachary , Beaubien Aldan , Johnson Ed , Goldy Jeff , Bolouri Hamid , Buckner Jane H. , Meijer Paul , Coffey Ernest M. , Skene Peter J. , Torgerson Troy R. , Li Xiao-jun , Bumol Thomas F.
Published: October 2020

Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The importance of these platforms in clinical and translational studies led us to investigate the impact of delayed blood processing on the numbers and state of peripheral blood mononuclear cells (PBMC) and on the plasma proteome. Similar to previous studies, we show minimal effects of delayed processing on the numbers and general phenotype of PBMCs up to 18 hours. In contrast, profound changes in the single-cell transcriptome and composition of the plasma proteome become evident as early as 6 hours after blood draw. These reflect patterns of cellular activation across diverse cell types that lead to progressive distancing of the gene expression state and plasma proteome from nativein vivobiology. Differences accumulating during an overnight rest (18 hours) could confound relevant biologic variance related to many underlying disease states.
Strain-level sample characterisation using long reads and MAPQ scores
Authors: Hall Grace A. , Speed Terence P. , Woodruff Christopher J.
Published: October 2020

Abstract

A simple but effective method for strain-level characterisation of microbial samples using long read data is presented. The method, which relies on having a non-redundant database of reference genomes, differentiates between strains within species and determines their relative abundance. It provides markedly better strain differentiation than that reported for the latest long read tools. Good estimates of relative abundances of highly similar strains present at less than 1% are achievable with as little as 1Gb of reads. Host contamination can be removed without great loss of sample characterisation performance. The method is simple and highly flexible, allowing it to be used for various different purposes, and as an extension of other characterisation tools. A code body implementing the underlying method is freely available.
Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules
Authors: Shams Arik , Higgins Sean A. , Fellmann Christof , Laughlin Thomas G. , Oakes Benjamin L. , Lew Rachel , Lukarska Maria , Arnold Madeline , Staahl Brett T. , Doudna Jennifer A. , Savage David F.
Published: October 2020

Proteins evolve through the modular rearrangement of elements known as domains. It is hypothesized that extant, multidomain proteins are the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for geneticminimization byiterativesize-exclusion andrecombination (MISER) that comprehensively assays all possible deletions of a protein. Using MISER, we generated a deletion landscape for the CRISPR protein Cas9. We found that Cas9 can tolerate large single deletions to the REC2, REC3, HNH, and RuvC domains, while still functioningin vitroandin vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.
Tautomerization constrains the accuracy of codon-anticodon decoding
Authors: Kazantsev Andriy , Ignatova Zoya
Published: October 2020

G○U(T) mismatch has the highest contribution to the error rate of base pair recognition in replication, as well as in codon-anticodon decoding in translation. Recently, this effect was unambiguously linked to keto-enol tautomerization, which enables the Watson-Crick (WC) geometry of the base pair. Structural studies of the ribosome revealing G○U in the WC geometry in the closed state of the A-site challenge the canonical induced-fit model of decoding and currently lack a physicochemical explanation.

Using computational and theoretical methods, we address effects of the ribosomal A-site on the wobble↔WC tautomerization reaction in G○U (wb-WC reaction), and the consequent implications for the decoding mechanism in translation. The free energy change of the wb-WC reaction in the middle codon-anticodon position was calculated with quantum-mechanical/molecular-mechanical umbrella sampling simulations. The wb-WC reaction was endoergic in the open A-site, but exoergic in the closed state. This effect can be explained in part by the decreased polarity of the closed A-site.

We developed a model of initial selection in translation that incorporates the wb-WC reaction parameters in the open and closed states of the A-site. In the new model, the exoergic wb-WC reaction is kinetically restricted by the decoding rates, which explains the observations of the WC geometry at equilibrium conditions. Moreover, the model reveals constraints imposed by the exoergic wb-WC reaction on the decoding accuracy: its equilibration counteracts the favorable contribution from equilibration of the open-closed transition. The similarity of the base-pair recognition mechanism in DNA polymerases allows extending this model to replication as well. Our model can be a step towards a general recognition model for flexible substrates.
Dysfunction of the histone demethylase IBM1 in Arabidopsis reshapes the root-associated bacteria community
Authors: Lv Suhui , Yang Yu , Peng Li , Tang Kai , Kaushal Richa , Zhang Huiming
Published: October 2020

Root-associated bacteria communities are influential to plant growth and stress tolerance. Epigenetic regulation plays important roles in many plant biological processes, but its potential impacts on the assembly of root microbiota remain unclear. Here we report that dysfunction of the histone demethylase IBM1 in Arabidopsis substantially alters root-associated soil bacteria community. We compared two alleles ofibm1mutant (ibm1-1andibm1-4) with wild type Arabidopsis regarding the root-associated bacteria community by 16S rRNA gene sequencing. The constrained principal coordinate analysis (PCoA) showed that theibm1mutants are both clearly separated from Col-0 along the major coordinates. Among the 29 families which have a relative abundance more than 0.5% in at least one sample, 10 and 11 families were commonly affected byibm1-1andibm1-4alleles in the rhizosphere and the endosphere compartment, respectively. Notably, the ACMs (Abundant Community members) belonging Pseudomonadaceae showed increased relative abundance in theibm1mutant alleles compared to Col-0 in both the rhizosphere and the endosphere compartments. The ACMs belonging to Oxalobacteraceae mostly showed decreased relative abundance inibm1mutants compared to Col-0 in endosphere compartment. These findings demonstrate an influential function of IBM1-mediated epigenetic regulation in shaping the root-associated microbiota.
Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in the entire postnatal and adult mouse brain
Authors: Wälchli Thomas , Bisschop Jeroen , Miettinen Arttu , Ulmann-Schuler Alexandra , Hintermüller Christoph , Meyer Eric P. , Krucker Thomas , Wälchli Regula , Monnier Philippe , Carmeliet Peter , Vogel Johannes , Stampanoni Marco
Published: October 2020

The formation of new blood vessels and the establishment of vascular networks are crucial during brain development, in the adult healthy brain, as well as in various diseases of the central nervous system (CNS). Here, we describe a method that enables hierarchical imaging and computational analysis of vascular networks in postnatal- and adult mouse brains. Resin-based vascular corrosion casting, scanning electron microscopy, synchrotron radiation and desktop µCT imaging, and computational network analysis are used. Combining these methods enables detailed visualization and quantification of the three-dimensional (3D) brain vasculature. Network features such as vascular volume fraction, branch point density, vessel diameter, - length, -tortuosity, and -directionality as well as extravascular distance can be obtained at any developmental stage from the early postnatal to the adult brain. Our method allows characterizing brain vascular networks separately for capillaries and non-capillaries.

The entire protocol, from mouse perfusion to vessel network analysis, takes approximately 10 days.

Online summary

This protocol uses vascular corrosion casting, hierarchical synchrotron radiation µCT imaging, and computational image analysis to assess the three-dimensional vascular network architecture.
SARS-CoV-2 genome-wide mapping of CD8 T cell recognition reveals strong immunodominance and substantial CD8 T cell activation in COVID-19 patients
Authors: Saini Sunil Kumar , Hersby Ditte Stampe , Tamhane Tripti , Povlsen Helle Rus , Hernandez Susana Patricia Amaya , Nielsen Morten , Gang Anne Ortved , Hadrup Sine Reker
Published: October 2020

To understand the CD8+T cell immunity related to viral protection and disease severity in COVID-19, we evaluated the complete SARS-CoV-2 genome (3141 MHC-I binding peptides) to identify immunogenic T cell epitopes, and determine the level of CD8+T cell involvement using DNA-barcoded peptide-major histocompatibility complex (pMHC) multimers. COVID-19 patients showed strong T cell responses, with up to 25% of all CD8+lymphocytes specific to SARS-CoV-2-derived immunodominant epitopes, derived from ORF1 (open reading frame 1), ORF3, and Nucleocapsid (N) protein. A strong signature of T cell activation was observed in COVID-19 patients, while no T cell activation was seen in the ‘non-exposed’ and ‘high exposure risk’ healthy donors. Interestingly, patients with severe disease displayed the largest T cell populations with a strong activation profile. These results will have important implications for understanding the T cell immunity to SARS-CoV-2 infection, and how T cell immunity might influence disease development.
High resolution and high throughput bacteria separation from blood using elasto-inertial microfluidics
Authors: Iyengar Sharath Narayana , Kumar Tharagan , Mårtensson Gustaf , Russom Aman
Published: October 2020

Improved sample preparation has the potential to address a huge unmet need for fast turnaround sepsis tests that enable early administration of appropriate antimicrobial therapy. In recent years, inertial and elasto-inertial microfluidics-based sample preparation has gained substantial interest for bioparticle separation applications. However, for applications in blood stream infections the throughput and bacteria separation efficiency has thus far been limited. In this work, for the first time we report elasto-inertial microfluidics-based bacteria isolation from blood at throughputs and efficiencies unparalleled with current microfluidics-based state of the art. In the method, bacteria-spiked blood sample is prepositioned close to the outer wall of a spiral microchannel using a viscoelastic sheath buffer. The blood cells will remain fully focused throughout the length of the channel while bacteria migrate to the inner wall for effective separation. Initially, particles of different sizes were used to investigate particle focusing and the separation performance of the spiral device. A separation efficiency of 96% for the 1 µm particles was achieved, while 100% of 3 µm particles were recovered at the desired outlet at a high throughput of 1 mL/min. Following, processing blood samples revealed a minimum of 1:2 dilution was necessary to keep the blood cells fully focus at the outer wall. In experiments involving bacteria spiked in diluted blood, viableE.coliwere continuously separated at a total flow rate of 1 mL/min, with an efficiency between 82 to 90% depending on the blood dilution. Using a single spiral, it takes 40 minutes to process 1 mL of blood at a separation efficiency of 82% and 3 hours at 90% efficiency. To the best of our knowledge, this is the highest blood sample throughput per single microfluidic chip reported for the corresponding separation efficiency. As such, the label-free, passive and high throughput bacteria isolation method has a great potential for speeding up downstream phenotypic and molecular analysis of bacteria.
Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution
Authors: Liakopoulos Apostolos , Aulin Linda B. S. , Buffoni Matteo , Fragkiskou Efthymia , van Hasselt J. G. Coen , Rozen Daniel E.
Published: October 2020

Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic-resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogenStreptococcus pneumoniaeby measuring collateral and fitness effects of clinically relevantgyrAandparCalleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how differentin silicocombination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of differentgyrAandparCalleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects to different antibiotics and suggest that these need to be considered in models examining CS-based therapies.

Significance

A promising strategy to overcome the evolution of antibiotic resistant bacteria is to use collateral sensitivity-informed antibiotic treatments that rely on cycling or mixing of antibiotics, such that that resistance towards one antibiotic confers increased sensitivity to the other. Here, focusing on multi-step fluoroquinolone resistance inStreptococcus pneumoniae, we show that antibiotic-resistance induces diverse collateral responses whose magnitude and direction are determined by allelic identity. Using mathematical simulations, we show that these effects can be exploited via combination treatment regimens to suppress thede novoemergence of resistance during treatment.
Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India
Authors: Laskar Rezwanuzzaman , Ali Safdar
Published: October 2020

The ongoing global pandemic of SARS-CoV-2 implies a corresponding accumulation of mutations. Herein the mutational status of 611 genomes from India along with their impact on proteins was ascertained. After excluding gaps and ambiguous sequences, a total of 493 variable sites (152 parsimony informative and 341 singleton) were observed. The most prevalent reference nucleotide was C (209) and substituted one was T (293). NSP3 had the highest incidence of 101 sites followed by S protein (74 sites), NSP12b (43 sites) and ORF3a (31 sites). The average number of mutations per sample for males and females was 2.56 and 2.88 respectively suggesting a higher contribution of mutations from females. Non-uniform geographical distribution of mutations implied by Odisha (30 samples, 109 mutations) and Tamil Nadu (31 samples, 40 mutations) suggests that sequences in some regions are mutating faster than others. There were 281 mutations (198 ‘Neutral’ and 83 ‘Disease’) affecting amino acid sequence. NSP13 has a maximum of 14 ‘Disease’ variants followed by S protein and ORF3a with 13 each. Further, constitution of ‘Disease’ mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2.
Winter activity of boreal bats
Authors: Blomberg Anna S. , Vasko Ville , Meierhofer Melissa B. , Johnson Joseph S. , Eeva Tapio , Lilley Thomas M.
Published: October 2020

Natural hibernation sites used by bats in areas that lack cave features have long remained unresolved. To investigate hibernation site selection and winter activity of boreal bats, we recorded bat calls using passive acoustic monitoring on 16 sites. These sites included four rock outcrops with crevices and cave features, three glacial erratics or boulder fields, three ancient shores, three root cellars and three control sites where we did not expect bats to be overwintering. Our results revealed echolocation calls ofEptesicus nilssonii,Plecotus auritusandMyotissp. We recorded significantly more activity near rock outcrops and root cellars compared to other habitats. We also found that ambient temperature had a positive effect on bat activity and found evidence thatP. auritusmay be using low barometric pressure as a proxy for suitable foraging conditions during the winter. Our results suggest that rock outcrops may be more important to bats than previously acknowledged, highlighting the need to take these sites in account in planning of conservation measures. Furthermore, our findings underline the suitability of using acoustic monitoring in homing on hibernation sites that are not otherwise accessible.
Newly isolated sporopollenin microcages fromCedrus libaniandPinus nigrafor controlled delivery of Oxaliplatin
Authors: Mujtaba Muhammad , Yılmaz Bahar Akyauz , Cansaran-Duman Demet , Akyuz Lalehan , Yangın Sevcan , Kaya Murat , Çeter Talip , Khawar Khalid Mahmood
Published: October 2020

Sporopollenin-mediated controlled drug delivery has been studied extensively owing to its physicochemical and biological charachteristics. In the present study, sporopollenin was successfully extracted from pollen grains ofC. libaniandP. nigrafollowed by the loading of a commonly known anticancer drug Oxaliplatin. Both the drug loading and physicochemical features were confirmed by using light microscopy, FT-IR, SEM and TGA. For the first time, real-time cell analyzer system, xCELLigence, was employed to record the Oxaliplatin-loaded and sporopollenin-mediated cell death (CaCo-2 and Vero cells) in real time. Both the assays confirmed the slow release of Oxaliplatin from sporopollenin for around 40–45 h. The expression of MYC andFOXO-3genes significantly increased in CaCo2 cell and decreased non-cancerous Vero cell confirming that sporopollenin-mediated controlled release of Oxaliplatin was promoting apoptosis cell death preventing the spread of its negative effects to nearby healthy cells. All the results suggested thatC. libaniandP. nigracould be suitable candidates for slow delivery of drugs.
Chlorophyll content and chlorophyll fluorescence as physiological parameters for monitoringOrobanche foetidaPoir. infestation on faba bean (Vicia fabaL.)
Authors: Amri Moez , Abbes Zouhaier , Trabelsi Imen , Ghanem Michel Edmond , Mentag Rachid , Kharrat Mohamed
Published: October 2020

In total, 39 faba bean (Vicia fabaL.) advanced lines were evaluated for resistance to broomrapeOrobanche foetidaunder highly infested field conditions. The trials were conducted during two consecutive copping seasons at Oued-Beja Research Station in Tunisia. The advanced lines XAR-VF00.13-1-2-1-2-1 and XBJ90.04-2-3-1-1-1-2A expressed high resistance level toO. foetidaexceeding those recorded for resistance checks Najeh and Baraca. Results showed thatO. foetidasignificantly affected the biomass, grain yield, chlorophyll content index (CCI) and the maximum quantum efficiency (Fv/Fmratio). No significant effect ofO. foetidaparasitism was observed on host plant water content (WC).O. foetidaparasitism significantly affected both CCI and Fv/Fmratio. CCI decreases varied from 46.4% for the susceptible check Badi and 4.2% and 9.3% observed for the genotypes Baraca and XBJ90.04-2-3-1-1-1-2A. Compared to susceptible check, slight decreases of Fv/Fmratio were observed for both advanced lines XBJ90.04-2-3-1-1-1-2A and XAR-VF00.13-1-2-1-2-1. Correlation between CCI and Fv/Fmwith the resistance to broomrape makes this, easy-to-measure, parameter very useful as a practical screening tool for early parasitism detection, diagnosis and identification and selection of high resistant plants against this pathogen.
Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation
Authors: Silver Anita , Perez Sean , Gee Melanie , Xu Bethany , Garg Shreeya , Will Kipling , Gill Aman
Published: October 2020

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study found that the ground beetle microbiome is consistent across different host food sources. We used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ:Anisodactylus similisLeConte, 1851,Pterostichus serripes(LeConte, 1875), andBrachinus elongatulusChaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets. Soil environment but not diet had a significant effect on bacterial diversity and composition. The three carabid species have patterns of microbial diversity similar to those previously found in other insect hosts. Metagenomic samples from two highly active tissue types — guts, and pygidial gland secretory cells (which produce defensive compounds) — were processed and sequenced separately from those of the remaining body. The observed similarity of the pygidial gland secretory cell microbiome across hosts suggests the possibility that it may be a conserved community, possibly due to functional interactions related to defensive chemistry. These results provide a baseline for future studies of the role of microbes in the diversification of defensive chemical biosynthesis in carabids.
Species composition and dynamics of aphids and parasitoid wasps in maize fields in Northeastern China
Authors: Zhang Ying , Zhao Min-chi , Cheng Jia , Liu Shuo , Yuan Hai-bin
Published: October 2020

Maize,Zea maysL., is the most abundant field crop in China. Aphids are the most economically damaging pest on maize, particularly in the cotton agri-ecosystems of Jilin Province, northern China. Parasitic wasps are important natural enemies of aphids, but limited information exists about their species composition, richness and seasonal dynamics in northern China. In this study, the population dynamics of maize aphids and parasitoid wasps were assessed in relation to each other during the summer seasons of two consecutive years, 2018 and 2019. We selected maize fields in the Changchun, Songyuan, Huinan and Gongzhuling areas of Jilin Province. Four species of aphids were recorded from these maize fields:Rhopalosiphum padi(L), Rhopalosiphum maidis(Fitch), Aphis gossypiiGlover andMacrosiphum miscanthi(Takahashi). The dominant species in each of the four areas wereR. maids(Filch) andR. padiin Changchun,R. padiin Songyuan,A. gossypiiandR. padiin Huinan, andA.gossypiiandR. padiin Gongzhuling. We delineated a species complex made up of primary parasitoids and hyperparasitoids associated with maize aphids. The primary parasitoidsLysiphlebus testaceipes, Binodoxys communisandAphelinus albipodustogether formed approximately 85.3% of the parasitoid complex.Pachyneuron aphidis, Phaenoglyphis villosa, Syrphophagus taeniatusandAsaphes suspensusmade up the hyperparasitoids. Of the primary parasitoids,L. testaceipeswas the dominant species (81.31%). Of the hyperparasitoid group,P. villosawas the dominant species (68.42%). Parasitism rates followed the fluctuation of the aphid population. The highest parasitic rate was observed during the peak period of cotton aphids. In this paper, the occurrence dynamics and dominant species of aphids and the dynamics of parasitic natural enemies of aphids in maize fields in Jilin Province are, for the first time, systematically reported. This study provides important information for the establishment and promotion of aphid biological control in maize fields.
Utilization and prospectus of non-timber forest products as livelihood materials
Authors: Das Atanu Kumar , Asaduzzaman Md. , Islam Md Nazrul
Published: October 2020

A study was conducted to find out the present utilization of non-timber forest products of the Sundarbans and tries to find out the alternative uses of these resources. The Sundarbans is the largest mangrove forest in the world and proper utilization of all resources can get a chance to manage this forest in sustainable way. A questionnaire survey was conducted to get information about the utilization of non-timber forest products. It has been found that about 87% of the people are fully dependent and 13% of the people are partially dependent on the Sundarbans. Among minor forest products, golpata, honey and fish were used by 92%, 93% and 82% of people, respectively. Most of the people are unknown about the alternative use of minor forest products but there is a great chance to use them for better purposes. Alternative uses of these products will help to improve the forest conditions as well as the socio-economic conditions of the people adjacent to the Sundarbans.