bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID-19 Pandemic and Thalassemia Major Patients: Transfusion Practice and Treatment Assessment
Authors: Oymak Yesim , Karapinar Tuba H.
Published: December 2020

Background:

When the COVID-19 epidemic occurred for the first time in December 2019, the governments worldwide took some restriction measures for slowing the spread of novel coronavirus. Eventually, there was a considerable decrease in volunteer blood donations. Regular transfusions and follow-up of patients with thalassemia major (TM) should be maintained during this period. It is possible that the treatment of the patients with TM may hinder due to the difficulty of reaching the treatment center and the difficulty of blood supply. Thus, in this study, we aimed to investigate whether there were any differences in the follow-up and treatment of the patients with TM during the outbreak.

Materials and Methods:

Sixty-one patients with TM who were followed up in our center without COVID-19 contact history and symptoms were included in this study. The demographic features and red blood cell volume per kilogram they received, pretransfusion hemoglobin, serum ferritin (SF) level, biochemical parameters, and transfusion interval were recorded. The difference between the arithmetic mean of the data before and during the pandemic was evaluated.

Results:

In this study, 61 patients with TM (32 males/29 females, mean age 13.9±6.8 y) were evaluated. The mean pretransfusion hemoglobin value was 9.14±0.77 g/dL and 8.87± 0.80 g/dL before and during the pandemic, respectively (P=0.023). There was no difference between before and during the pandemic concerning transfusion interval and transfusion volume. However, SF levels increased above 1000 ng/mL in 16.6% of patients.

Conclusion:

Although blood donation decreased significantly during the pandemic, it was observed in this study that the blood needs of patients with TM could be provided. The results of the SF level showed that the management of chelation therapy should be more meticulous. However, we should be ready for the challenges in the transfusion practice of patients with TM due to fluctuations in the COVID-19 pandemic.
Low Concordance Between Pediatric Emergency Attendings and Pediatric Residents for Predictors of Serious Intracranial Injury
Authors: Duncan Ellen , Mojica Michael , Ching Kevin , Harwayne-Gidansky Ilana
Published: December 2020

Objectives

Minor head trauma is a common cause of pediatric emergency room visits. The Pediatric Emergency Care Applied Research Network head trauma clinical decision rules (PECARN-CDR) are designed to assist clinicians in determining which patients require imaging. However, only minimal data are available on the accuracy of residents' assessments using PECARN-CDR. Prior research suggests that trainees often come to erroneous conclusions about pediatric head trauma. The objective of the present study was to assess concordance between pediatric residents' and attending physicians' assessments of children with low-risk head trauma, with the ultimate goal of improving education in pediatric trauma assessment.

Methods

This is a retrospective cohort study analyzing concordance between pediatric residents and pediatric emergency attendings who provided PECARN-CDR–based evaluations of low-risk head injuries. It is a planned subanalysis based on a prospectively collected, multicenter data set tracking pediatric head trauma encounters from July 2014 to June 2019.

Results

Data were collected from 436 pediatric residents, who encountered 878 patients. In the case of patients younger than 2 years, low concordance between residents and attendings was observed for the following elements of the PECARN-CDR: severe mechanism (κ = 0.24), palpable skull fracture (κ = 0.23), Glasgow Coma Scale (GCS) score less than 15 (κ = 0.14), and altered mental status (AMS; κ = −0.03). There was moderate to high agreement between residents and attendings for loss of consciousness (κ = 0.71), nonfrontal hematoma (κ = 0.48), and not acting normally per parent (κ = 0.35). In the case of patients older than 2 years, there was low concordance for signs of basilar skull fracture (κ = 0.28) and GCS score less than 15 (κ = 0.10). Concordance was high to moderate for history of vomiting (κ = 0.88), loss of consciousness (κ = 0.67), severe headache (κ = 0.50), severe mechanism (κ = 0.44), and AMS (κ = 0.42). Residents were more conservative, that is, more likely to report a positive finding, in nearly all components of the PECARN-CDR.

Conclusions

Resident assessment of children presenting to the ED with minor head trauma is often poorly concordant with attending assessment on the major predictors of clinically important traumatic brain injury (abnormal GCS, AMS, signs of skull fracture) based on the PECARN-CDR. Future work may explore the reasons for low concordance and seek ways to improve pediatric resident education in the diagnosis and management of trauma.
Improving Intubation Success in Pediatric and Neonatal Transport Using Simulation
Authors: Dalrymple Hannah Mary , Browning Carmo Kathryn
Published: December 2020

Background

Pediatric and neonatal first-pass intubation rates are higher in adult trained retrieval services than in neonatal or pediatric trained services. Some authors have attributed this to more frequent opportunities to practice the skill in the adult population.

Objective

The aim of this study was to increase the first-pass intubation rate without adverse events by introducing daily intubation simulation at our mixed neonatal and pediatric retrieval service.

Methods

This prospective cohort study performed from July to December 2018 in our mixed neonatal and pediatric retrieval service involved 16 medical staff performing simulated intubation at commencement of their retrieval shift with a retrieval nurse. Checklists for neonatal and pediatric intubation were introduced to the retrieval service for the intervention cohort. Participants were asked to complete questionnaires about intubation performed on retrieval to gather data not routinely collected by the service.

Results

Seven hundred and sixty-eight patients were retrieved by the service and 70 patients required intubation by the retrieval team during the intervention period. First-pass intubation rates were higher during the intervention period compared with a historical cohort, despite less intubations being performed overall. First-pass intubation rates improved from 59% to 78% in neonatal patients (P = 0.032), 58% to 65% in pediatric patients (P = 0.68) and from 58% to 74% overall (P = 0.043). There were no severe adverse events detected during the intervention period. Minor adverse events were associated with multiple attempts at intubation (P < 0.001). Overall compliance with simulation protocol was 43.5%, and on average, each doctor completed simulation once per month.

Conclusions

Simulation is a useful adjunct to support neonatal and pediatric intubation training in the current environment of reducing intubation frequency.
A Heterogeneity Radiomic Nomogram for Preoperative Differentiation of Primary Gastric Lymphoma From Borrmann Type IV Gastric Cancer
Authors: Feng Bao , Huang Liebin , Li Changlin , Quan Yong , Chen Yehang , Xue Huimin , Chen Qinxian , Sun Shanlin , Li Ronggang , Long Wansheng
Published: December 2020

Objective

This study aimed to preoperatively differentiate primary gastric lymphoma from Borrmann type IV gastric cancer by heterogeneity nomogram based on routine contrast-enhanced computed tomographic images.

Methods

We enrolled 189 patients from 2 hospitals (90 in the training cohort and 99 in the validation cohort). Subjective findings, including high-enhanced mucosal sign, high-enhanced serosa sign, nodular or an irregular outer layer of the gastric wall, and perigastric fat infiltration, were assessed to construct a subjective finding model. A deep learning model was developed to segment tumor areas, from which 1680 three-dimensional heterogeneity radiomic parameters, including first-order entropy, second-order entropy, and texture complexity, were extracted to build a heterogeneity signature by least absolute shrinkage and selection operator logistic regression. A nomogram that integrates heterogeneity signature and subjective findings was developed by multivariate logistic regression. The diagnostic performance of the nomogram was assessed by discrimination and clinical usefulness.

Results

High-enhanced serosa sign and nodular or an irregular outer layer of the gastric wall were identified as independent predictors for building the subjective finding model. High-enhanced serosa sign and heterogeneity signature were significant predictors for differentiating the 2 groups (all, P < 0.05). The area under the curve with heterogeneity nomogram was 0.932 (95% confidence interval, 0.863–0.973) in the validation cohort. Decision curve analysis and stratified analysis confirmed the clinical utility of the heterogeneity nomogram.

Conclusions

The proposed heterogeneity radiomic nomogram on contrast-enhanced computed tomographic images may help differentiate primary gastric lymphoma from Borrmann type IV gastric cancer preoperatively.
Use of a Dual Artificial Intelligence Platform to Detect Unreported Lung Nodules
Authors: Yen Andrew , Pfeffer Yitzi , Blumenfeld Aviel , Balcombe Jonathan N. , Berland Lincoln L. , Tanenbaum Lawrence , Kligerman Seth J.
Published: December 2020

Objective

To investigate the performance of Dual-AI Deep Learning Platform in detecting unreported pulmonary nodules that are 6 mm or greater, comprising computer-vision (CV) algorithm to detect pulmonary nodules, with positive results filtered by natural language processing (NLP) analysis of the dictated report.

Methods

Retrospective analysis of 5047 chest CT scans and corresponding reports. Cases which were both CV algorithm positive (nodule ≥ 6 mm) and NLP negative (nodule not reported), were outputted for review by 2 chest radiologists.

Results

The CV algorithm detected nodules that are 6 mm or greater in 1830 (36.3%) of 5047 cases. Three hundred fifty-five (19.4%) were unreported by the radiologist, as per NLP algorithm. Expert review determined that 139 (39.2%) of 355 cases were true positives (2.8% of all cases). One hundred thirty (36.7%) of 355 cases were unnecessary alerts—vague language in the report confounded the NLP algorithm. Eighty-six (24.2%) of 355 cases were false positives.

Conclusions

Dual-AI platform detected actionable unreported nodules in 2.8% of chest CT scans, yet minimized intrusion to radiologist's workflow by avoiding alerts for most already-reported nodules.
Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China
Authors: Xue Qiong , Zuo Zhenqiang , Zhou Heng , Zhou Jian , Zhang Shengjie , Han Jing , Zhao Dahe , Xiang Hua
Published: December 2020

A haloalkaliphilic strain XQ-INN 246T was isolated from the sediment of a salt pond in Inner Mongolia Autonomous Region, China. Cells of the strain were rods, motile and strictly aerobic. The strain was able to grow in the presence of 2.6–5.3 M NaCl (optimum concentration is 4.4 M) at 30–50 °C (optimum temperature is 42 °C) and pH 7.0–10.0 (optimum pH is 8.0–8.5). The whole genome sequencing of strain XQ-INN 246T revealed a genome size of 4.52 Mbp and a DNA G+C content of 62.06 mol%. Phylogenetic tree based on 16S rRNA gene sequences and concatenated amino acid sequences of 122 single-copy conserved proteins revealed a robust lineage of the strain XQ-INN 246T with members of related genera of the family

Natrialbaceae

. The strain possessed the polar lipids of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Based on phylogenetic analysis, phenotypic characteristics, chemotaxonomic properties and genome relatedness, the isolate was proposed as the type strain of a novel species of a new genus within the family Natrialbaceae, for which the name Salinadaptatus halalkaliphilus gen. nov., sp. nov. is proposed. The type strain is XQ-INN 246T (=CGMCC 1.16692T=JCM 33751T).
Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019
Authors: Xiaoli Lingzi , Benoliel Eileen , Peng Yanhui , Aneke Janessa , Cassiday Pamela K. , Kay Meagan , McKeirnan Shelly , Duchin Jeffery S. , Kawakami Vance , Lindquist Scott , Acosta Anna M. , DeBolt Chas , Tondella Maria Lucia , Weigand Michael R.
Published: December 2020

Between July 2018 and May 2019,

Corynebacterium diphtheriae

was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were microbiologically identified as nontoxigenic

C. diphtheriae

biovar mitis. Whole-genome sequencing confirmed that all case isolates were genetically related, associated with sequence type 445 and differing by fewer than 24 single-nucleotide polymorphisms (SNPs). Compared to publicly available

C. diphtheriae

genomic data, these WA isolates formed a discrete cluster with SNP variation consistent with previously reported outbreaks. Virulence-related gene content variation within the highly related WA cluster isolates was also observed. These results indicated that genome characterization can readily support epidemiology of nontoxigenic

C. diphtheriae

.
Divergence in bidirectional plant-soil feedbacks between montane annual and coastal perennial ecotypes of yellow monkeyflower (Mimulus guttatus)
Authors: McIntosh Mariah M. , Bullington Lorinda , Lekberg Ylva , Fishman Lila
Published: December 2020

Understanding the physiological and genetic mechanisms underlying plant variation in interactions with root-associated biota (RAB) requires a micro-evolutionary approach. We use locally adapted montane annual and coastal perennial ecotypes ofMimulus guttatus(yellow monkeyflower) to examine population-scale differences in plant-RAB-soil feedbacks.

We characterized fungal communities for the two ecotypesin-situand used a full-factorial greenhouse experiment to investigate the effects of plant ecotype, RAB source, and soil origin on plant performance and endophytic root fungal communities.

The two ecotypes harbored different fungal communities and responsiveness to soil biota was highly context-dependent. Soil origin, RAB source, and plant ecotype all affected the intensity of biotic feedbacks on plant performance. Feedbacks were primarily negative, and we saw little evidence of local adaptation to either soils or RAB. Both RAB source and soil origin significantly shaped fungal communities in roots of experimental plants. Further, the perennial ecotype was more colonized by arbuscular mycorrhizal fungi (AMF) than the montane ecotype, and preferentially recruited home AMF taxa.

Our results suggest life history divergence and distinct edaphic habitats shape plant responsiveness to RAB and influence specific associations with potentially mutualistic root endophytic fungi. Our results advance the mechanistic study of intraspecific variation in plant–soil–RAB interactions.
Traditionally used aqueous herbal extracts for respiratory ailments exhibit anti-inflammatory activity
Authors: Kannian Priya , Mohana Sambasivam , Vishwarohini Manivasagam , Saleem Abdul Rahim Mohamed
Published: December 2020

Background

Phytoconstituents from plants provide a huge array of medicinal properties and have been used for many centuries as household medicines in India to treat respiratory illnesses. There are limited studies on comprehensive evaluations of these plant extracts to understand their healing properties.

Aim

To evaluate the antimicrobial and immunomodulatory properties of the 10 commonly used medicinal plants to treat respiratory illnesses in a comprehensive manner.

Materials & Methods

The acetone, ethanol and aqueous extracts from the 10 plants were evaluated for antiviral, antifungal and antibacterial activity. Additionally, the aqueous extracts were also evaluated for immunomodulatory properties.

Results

None of the extracts exhibited antiviral activity against the four influenza viruses, antifungal activity againstCandida albicansor antibacterial activity against Gram negative bacilli. Eight acetone extracts, nine ethanol extracts and one aqueous extract(NSAq)exhibited antibacterial activity at concentrations below 1mg/ml againstS. pyogenesand/orS. pneumoniae.All the aqueous extracts exhibited dose-dependent anti-inflammatory activity against the innate immunity cytokines, TNF-α and IL-1β, and the Th1 cytokine, IFN-γ, but not against the Th2 cytokine, IL-4.

Conclusions

Overall the study elucidates that the acetone and ethanol extracts exhibit antibacterial activity, while the commonly consumed aqueous extracts ameliorate respiratory illnesses through immune modulation.
Scale-free dynamics in animal groups and brain networks
Authors: Ribeiro Tiago L. , Chialvo Dante R. , Plenz Dietmar
Published: December 2020

Collective phenomena fascinate by the emergence of order in systems composed of a myriad of small entities. They are ubiquitous in nature and can be found over a vast range of scales in physical and biological systems. Their key feature is the seemingly effortless emergence of adaptive collective behavior that cannot be trivially explained by the properties of the system’s individual components. This perspective focuses on recent insights into the similarities of correlations for two apparently disparate phenomena: flocking in animal groups and neuronal ensemble activity in the brain. We first will summarize findings on the spontaneous organization in bird flocks and macro-scale human brain activity utilizing correlation functions and insights from critical dynamics. We then will discuss recent experimental findings that apply these approaches to the collective response of neurons to visual and motor processing, i.e. to local perturbations of neuronal networks at the meso- and microscale. We show how scale-free correlation functions capture the collective organization of neuronal avalanches in evoked neuronal populations in nonhuman primates and between neurons during visual processing in rodents. These experimental findings suggest that the coherent collective neural activity observed at scales much larger than the length of the direct neuronal interactions is demonstrative of a phase transition. We discuss the experimental support for either discontinuous or continuous phase transitions. We conclude that at or near a phase-transition neuronal information can propagate in the brain with the same efficiency as proposed to occur in the collective adaptive response observed in some animal groups.
Molecular pathways to high-level azithromycin resistance inNeisseria gonorrhoeae
Authors: Laumen J.G.E. , Manoharan-Basil S.S. , Verhoeven E , Abdellati S , De Baetselier I , Crucitti T , Xavier B.B. , Chapelle S , Lammens C , Van Dijck C , Malhotra-Kumar S , Kenyon C
Published: December 2020

Objectives

The prevalence of azithromycin resistance inNeisseria gonorrhoeaeis increasing in numerous populations worldwide. The aim of this study was to characterize the genetic pathways leading to high-level azithromycin resistance.

Methods

A customized morbidostat was used to subject twoN. gonorrhoeaereference strains (WHO-F and WHO-X) to dynamically sustained azithromycin pressure. We tracked stepwise evolution of resistance by whole genome sequencing.

Results

Within 26 days, all cultures evolved high-level azithromycin resistance. Typically, the first step towards resistance was found in transitory mutations in genesrplD,rplVandrpmH(encoding the ribosomal proteins L4, L22 and L34 respectively), followed by mutations in the MtrCDE-encoded efflux pump and the 23S rRNA gene. Low-to high-level resistance was associated with mutations in the ribosomal proteins and MtrCDE-encoded efflux pump. However, high-level resistance was consistently associated with mutations in the 23S ribosomal RNA - mainly the well-known A2059G and C2611T mutations, but also at position A2058G.

Conclusions

This study enabled us to track previously reported mutations and identify novel mutations in ribosomal proteins (L4, L22 and L34) that may play a role in the genesis of azithromycin resistance inN. gonorrhoeae.
Mouse and Human Antibodies that Bind HLA-E-Leader Peptide Complexes and Enhance NK Cell Cytotoxicity
Authors: Li Dapeng , Brackenridge Simon , Walters Lucy C. , Swanson Olivia , Harlos Karl , Rozbesky Daniel , Cain Derek W. , Wiehe Kevin , Scearce Richard M. , Barr Maggie , Mu Zekun , Parks Robert , Quastel Max , Edwards Robert J. , Wang Yunfei , Rountree Wes , Saunders Kevin O. , Ferrari Guido , Borrow Persephone , Yvonne Jones E. , Munir Alam S. , Azoitei Mihai L. , Gillespie Geraldine M. , McMichael Andrew J. , Haynes Barton F.
Published: December 2020

HLA-E is a non-classical class Ib molecule that has limited polymorphism and binds HLA class Ia leader peptides (VL9). HLA-E-VL9 complexes interact with the natural killer (NK) cell receptors NKG2A-C/CD94 and regulate NK cell-mediated cytotoxicity. Here we isolated a murine IgM antibody 3H4, that specifically recognized HLA-E-VL9 bound complexes and enhanced killing of HLA-E-VL9-expressing cells by an NKG2A+NK cell line. Structural analysis revealed how 3H4 prevents CD94/NKG2A docking on HLA-E-VL9 by binding with an overlapping footprint. Uponin vitromaturation, an affinity-optimized 3H4 IgG showed enhanced NK killing of HLA-E-VL9-expressing cells. Remarkably, HLA-E-VL9-specific IgM autoantibodies with similar specificity and functions to 3H4 were subsequently isolated from naïve B cells of cytomegalovirus (CMV)-negative, healthy male human donors. Thus, a repertoire of germline low affinity HLA-E-VL9-reactive antibodies are present in both naïve human and murine B cell repertoires. These antibodies can enhance NK cell cytotoxicity and therefore have potential for therapeutic modulation of NK cell function.
Early or late gestational exposure to maternal immune activation alters neurodevelopmental trajectories in mice: an integrated neuroimaging, behavioural, and transcriptional study
Authors: Guma Elisa , Bordignon Pedro , Devenyi Gabriel A. , Gallino Daniel , Anastassiadis Chloe , Cvetkovska Vedrana , Barry Amadou , Snook Emily , Germann Jurgen , Greenwood Celia M.T. , Misic Bratislav , Bagot Rosemary C. , Chakravarty M. Mallar
Published: December 2020

Prenatal maternal immune activation (MIA) is a risk factor for neurodevelopmental disorders. How gestational timing of MIA-exposure differentially impacts downstream development remains unclear. Here, we characterize neurodevelopmental trajectories of mice exposed to MIA induced by poly I:C either early (gestational day [GD]9) or late (GD17) in gestation using longitudinal structural magnetic resonance imaging from weaning to adulthood. Early MIA-exposure associated with accelerated brain volume increases in adolescence/early-adulthood that normalized in later adulthood, in regions including the striatum, hippocampus, and cingulate cortex. Similarly, alterations in anxiety, stereotypic, and sensorimotor gating behaviours observed in adolescence normalized in adulthood. In contrast, MIA-exposure in late gestation had less impact on anatomical and behavioural profiles. Using a multivariate technique to relate imaging and behavioural variables for the time of greatest alteration, i.e. adolescence/early adulthood, we demonstrate that variation in anxiety, social, and sensorimotor gating associates significantly with volume of regions including the dorsal and ventral hippocampus, and anterior cingulate cortex. Using RNA sequencing to explore the molecular underpinnings of region-specific alterations in early MIA-exposed mice in adolescence, we observed the most transcriptional changes in the dorsal hippocampus, with regulated genes enriched for fibroblast growth factor regulation, autistic behaviours, inflammatory pathways, and microRNA regulation. This indicates that MIA in early gestation perturbs brain development mechanisms implicated in neurodevelopmental disorders. Our findings demonstrate the inherent strength of an integrated hypothesis- and data-driven approach in linking brain-behavioural alterations to the transcriptome to understand how MIA confers risk for major mental illness.
Hebbian plasticity in parallel synaptic pathways: A circuit mechanism for systems memory consolidation
Authors: Remme Michiel , Bergmann Urs , Alevi Denis , Schreiber Susanne , Sprekeler Henning , Kempter Richard
Published: December 2020

Systems memory consolidation involves the transfer of memories across brain regions and the transformation of memory content. For example, declarative memories that transiently depend on the hippocampal formation are transformed into long-term memory traces in neocortical networks, and procedural memories are transformed within cortico-striatal networks. These consolidation processes are thought to rely on replay and repetition of recently acquired memories, but the cellular and network mechanisms that mediate the changes of memories are poorly understood. Here, we suggest that systems memory consolidation could arise from Hebbian plasticity in networks with parallel synaptic pathways — two ubiquitous features of neural circuits in the brain. We explore this hypothesis in the context of hippocampus-dependent memories. Using computational models and mathematical analyses, we illustrate how memories are transferred across circuits and discuss why their representations could change. The analyses suggest that Hebbian plasticity mediates consolidation by transferring a linear approximation of a previously acquired memory into a parallel pathway. Our modelling results are further in quantitative agreement with lesion studies in rodents. Moreover, a hierarchical iteration of the mechanism yields power-law forgetting — as observed in psychophysical studies in humans. The predicted circuit mechanism thus bridges spatial scales from single cells to cortical areas and time scales from milliseconds to years.

Author summary

After new memories are acquired, they can be transferred over time into other brain areas — a process called systems memory consolidation. For example, new declarative memories, which refer to the conscious memory of facts and events, depend on the hippocampus. Older declarative memories, however, also rely on neocortical networks. The cellular mechanisms underlying such a transfer are poorly understood. In this work, we show that a simple and in the brain ubiquitous connectivity pattern, combined with a standard learning rule, leads to gradual memory transfer. We illustrate our proposed mechanism in numerical simulations and mathematical analyses. At the neurophysiological level, our theory explains experimental findings on memory storage in the hippocampal formation when specific pathways between neural populations are disrupted. At the psychophysical level, we can account for the power-law forgetting curves typically found in humans. A consequence of the proposed model is that consolidated memories can yield faster responses because they are stored in increasingly shorter synaptic pathways between sensory and motor areas. By giving a mechanistic explanation of the consolidation process, we contribute to the understanding of the transfer of memories and the reorganization of memories over time.
Using a non-destructive sugar-feeding assay for sporozoite detection and estimating the extrinsic incubation period ofPlasmodium falciparumin mosquito vectors
Authors: Guissou Edwige , Waite Jessica L. , Jones Matthew , Bell Andrew S. , Suh Eunho , Yameogo Koudraogo B. , Djegbe Nicaise , Da Dari F. , Hien Domonbabele FdS , Yerbanga Rakiswende S. , Ouedraogo Anicet G. , Dabiré Kounbobr R. , Cohuet Anna , Thomas Matthew B. , Lefèvre Thierry
Published: December 2020

Despite its epidemiological importance, the timePlasmodiumparasites take to achieve development in the vector mosquito (the extrinsic incubation period, EIP) remains poorly characterized. A novel non-destructive assay designed to estimate EIP in single mosquitoes, and more broadly to studyPlasmodium–Anophelesvectors interactions, is presented. The assay uses small pieces of cotton wool soaked in sugar solution to collect malaria sporozoites from individual mosquitoes during sugar feeding to monitor infection status over time. This technique has been tested across four natural malaria mosquito species of Africa and Asia, six parasite isolates ofPlasmodium falciparum, and across a range of temperatures relevant to malaria transmission in field conditions. We find that monitoring individual infectious mosquitoes is feasible, although due to the frequency of mosquito sugar feeding and inter-individual variation in infection intensity, there is inherent risk that this technique will result in some false negatives. The sensitivity rate ranged from 0.27 to 0.81 depending on mosquito species and on infection intensity in mosquitoes used to collect saliva. Using this non-destructive technique, the estimated median extrinsic incubation period ofP. falciparumat 27°C was 11 to 14 days depending on mosquito species and parasite isolate. Long-term individual tracking also revealed that sporozoite transfer onto cotton wool can occur at least until day 40 post-infection. In addition to contributing to a better understanding of EIP and mosquito to human transmission with implications for improving epidemiological models, this technique also allows to link different transmission traits at the mosquito individual level. As one example, we found a significant relationship between EIP and mosquito lifespan, with short individual EIP associated with short mosquito lifespan. Correlations between mosquito/parasite traits often reveal trade-offs and constraints and have important implications for understanding the evolution of parasite transmission strategies.
An Omic and Multidimensional Spatial Atlas from Serial Biopsies of an Evolving Metastatic Breast Cancer
Authors: Johnson Brett E. , Creason Allison L. , Stommel Jayne M. , Keck Jamie M. , Parmar Swapnil , Betts Courtney B. , Blucher Aurora , Boniface Christopher , Bucher Elmar , Burlingame Erik , Camp Todd , Chin Koei , Eng Jennifer , Estabrook Joseph , Feiler Heidi S. , Hu Zhi , Kolodzie Annette , Kong Ben L. , Labrie Marilyne , Lee Jinho , Leyshock Patrick , Mitri Souraya , Patterson Janice , Riesterer Jessica L. , Sivagnanam Shamilene , Somers Julia , Sudar Damir , Thibault Guillaume , Zheng Christina , Nan Xiaolin , Heiser Laura M. , Spellman Paul T. , Thomas George , Demir Emek , Chang Young Hwan , Coussens Lisa M. , Guimaraes Alexander R. , Corless Christopher , Goecks Jeremy , Bergan Raymond , Mitri Zahi , Mills Gordon B. , Gray Joe W.
Published: December 2020

Mechanisms of therapeutic resistance manifest in metastatic cancers as tumor cell intrinsic alterations and extrinsic microenvironmental influences that can change during treatment. To support the development of methods for the identification of these mechanisms in individual patients, we present here an Omic and Multidimensional Spatial (OMS) Atlas generated from four serial biopsies of a metastatic breast cancer patient during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata including treatment times and doses, anatomic imaging, and blood-based response measurements to exploratory analytics including comprehensive DNA, RNA, and protein profiles, images of multiplexed immunostaining, and 2- and 3-dimensional scanning electron micrographs. These data reveal aspects of therapy-associated heterogeneity and evolution of the cancer’s genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples showing how integrative analyses of these data provide insights into potential mechanisms of response and resistance, and suggest novel therapeutic vulnerabilities.
Single Cell Sequencing Reveals Glial Specific Responses to Tissue Processing & Enzymatic Dissociation in Mice and Humans
Authors: Marsh Samuel E. , Kamath Tushar , Walker Alec J. , Dissing-Olesen Lasse , Hammond Timothy R. , Young Adam M.H. , Abdulraouf Abdulraouf , Nadaf Naeem , Dufort Connor , Murphy Sarah , Kozareva Velina , Vanderburg Charles , Hong Soyon , Bulstrode Harry , Hutchinson Peter J. , Gaffney Daniel J. , Franklin Robin J.M. , Macosko Evan Z. , Stevens Beth
Published: December 2020

A key aspect of nearly all single cell experiments is the necessity to dissociate intact tissues into single cell suspensions for processing. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have onex vivogene expression changes during this process. Microglia, the brain’s resident macrophages, are a highly dynamic population that are extremely sensitive to their microenvironment and have been shown to dramatically alter their transcriptome upon stimulation. We demonstrate that use of enzymatic dissociation methods on mouse central nervous system (CNS) tissue induces an aberrant gene expression signature in microglia that can significantly confound downstream analysis. To minimize this issue, we developed a flexible protocol, that can be used with existing enzymatic protocols for fresh tissue, to eliminate artifactual gene expression while allowing for increased cell type diversity and yield. We demonstrate efficacy of this protocol in analysis of diverse CNS cell types and sorted myeloid populations while using enzymatic dissociation. Generation of new and reanalysis of previously published human brain single nucleus RNAseq (snRNA-seq) datasets reveal that a similar signature is also present in post-mortem tissue. Through novel snRNA-seq analysis of acutely-resected neurosurgical tissue we demonstrate that this signature can be induced in human tissue due to technical differences in sample processing. These results provide key insight into the potential confounds of enzymatic digestion and provide a solution to allow for enzymatic digestion for scRNA-seq while avoidingex vivotranscriptional artifacts. Analysis of human tissue reveals potential for artifacts in current and future snRNA-seq datasets that will require deeper analysis and careful consideration to separate true biology from artifacts related to post-mortem processes.
MASiVar: Multisite, Multiscanner, and Multisubject Acquisitions for Studying Variability in Diffusion Weighted Magnetic Resonance Imaging
Authors: Cai Leon Y. , Yang Qi , Kanakaraj Praitayini , Nath Vishwesh , Newton Allen T. , Edmonson Heidi A. , Luci Jeffrey , Conrad Benjamin N. , Price Gavin R. , Hansen Colin B. , Kerley Cailey I. , Ramadass Karthik , Yeh Fang-Cheng , Kang Hakmook , Garyfallidis Eleftherios , Descoteaux Maxime , Rheault Francois , Schilling Kurt G. , Landman Bennett A.
Published: December 2020

Purpose

Diffusion weighted imaging (DWI) allows investigators to identify structural, microstructural, and connectivitybased differences between subjects, but variability due to session and scanner biases is a challenge.

Methods

To investigate DWI variability, we present MASiVar, a multisite dataset consisting of 319 diffusion scans acquired at 3T from b = 1000 to 3000 s/mm2 across 14 healthy adults, 83 healthy children (5 to 8 years), three sites, and four scanners as a publicly available, preprocessed, and de-identified dataset. With the adult data, we demonstrate the capacity of MASiVar to simultaneously quantify the intrasession, intersession, interscanner, and intersubject variability of four common DWI processing approaches: (1) a tensor signal representation, (2) a multi-compartment neurite orientation dispersion and density model, (3) white matter bundle segmentation, and (4) structural connectomics. Respectively, we evaluate region-wise fractional anisotropy (FA), mean diffusivity, and principal eigenvector; region-wise cerebral spinal fluid volume fraction, intracellular volume fraction, and orientation dispersion index; bundle-wise shape, volume, FA, and length; and whole connectome correlation and maximized modularity, global efficiency, and characteristic path length.

Results

We plot the variability in these measures at each level and find that it consistently increases with intrasession to intersession to interscanner to intersubject effects across all processing approaches and that sometimes interscanner variability can approach intersubject variability.

Conclusions

This study demonstrates the potential of MASiVar to more globally investigate DWI variability across multiple levels and processing approaches simultaneously and suggests harmonization between scanners for multisite analyses should be considered prior to inference of group differences on subjects.
A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients by phage display is binding to the ACE2-RBD interface and is tolerant to most known recently emerging RBD mutations
Authors: Bertoglio Federico , Fühner Viola , Ruschig Maximilian , Heine Philip Alexander , Abasi Leila , Klünemann Thomas , Rand Ulfert , Meier Doris , Langreder Nora , Steinke Stephan , Ballmann Rico , Schneider Kai-Thomas , Ralph Roth Kristian Daniel , Kuhn Philipp , Riese Peggy , Schäckermann Dorina , Korn Janin , Koch Allan , Chaudhry M. Zeeshan , Eschke Kathrin , Kim Yeonsu , Zock-Emmenthal Susanne , Becker Marlies , Scholz Margitta , Schmidt Garcia Moreira Gustavo Marçal , Wenzel Esther Veronika , Russo Giulio , Garritsen Hendrikus S.P. , Casu Sebastian , Gerstner Andreas , Roth Günter , Adler Julia , Trimpert Jakob , Hermann Andreas , Schirrmann Thomas , Dübel Stefan , Frenzel André , Van den Heuvel Joop , Čičin-Šain Luka , Schubert Maren , Hust Michael
Published: December 2020

The novel betacoranavirus SARS-CoV-2 causes a form of severe pneumonia disease, termed COVID-19 (coronavirus disease 2019). Recombinant human antibodies are proven potent neutralizers of viruses and can block the interaction of viral surface proteins with their host receptors. To develop neutralizing anti-SARS-CoV-2 antibodies, antibody gene libraries from convalescent COVID-19 patients were constructed and recombinant antibody fragments (scFv) against the receptor binding domain (RBD) of the S1 subunit of the viral spike (S) protein were selected by phage display. The selected antibodies were produced in the scFv-Fc format and 30 showed more than 80% inhibition of spike (S1-S2) binding to cells expressing ACE2, assessed by flow cytometry screening assay. The majority of these inhibiting antibodies are derived from the VH3-66 V-gene. The antibody STE90-C11 showed a sub nM IC50 in a plaque-based live SARS-CoV-2 neutralization assay. Thein vivoefficacy of the antibody was demonstrated in the Syrian hamster and in the hACE2 mice model using a silenced human IgG1 Fc part. The crystal structure of STE90-C11 Fab in complex with SARS-CoV-2-RBD was solved at 2.0 Å resolution showing that the antibody binds at the same region as ACE2 to RBD. The binding and inhibtion of STE90-C11 is not blocked by many known RBD mutations including N439K, L452R, E484K or L452R+E484Q (emerging B.1.617). STE90-C11 derived human IgG1 with FcγR silenced Fc (COR-101) is currently undergoing Phase Ib/II clinical trials for the treatment of moderate to severe COVID-19.

In Brief

Human antibodies were selected from convalescent COVID-19 patients using antibody phage display. The antibody STE90-C11 is neutralizing authentic SARS-CoV-2 virusin vitroandin vivoand the crystal structure of STE90-C11 in complex with SARS-CoV-2-RBD revealed that this antibody is binding in the RBD-ACE2 interface. S1 binding of STE90-C11 and inhibition of ACE2 binding is not blocked by many known RBD mutations.
A mechanistic model for reward prediction and extinction learning in the fruit fly
Authors: Springer Magdalena , Nawrot Martin Paul
Published: December 2020

Extinction learning, the ability to update previously learned information by integrating novel contradictory information, is a key mechanism for adapting our behavior and of high clinical relevance for therapeutic approaches to the modulation of maladaptive memories. Insect models have been instrumental in uncovering fundamental processes of memory formation and memory update. Recent experimental results inDrosophila melanogastersuggest that, after the behavioral extinction of a memory, two parallel but opposing memory traces coexist, residing at different sites within the mushroom body. Here we propose a minimalistic circuit model of theDrosophilamushroom body that supports classical appetitive and aversive conditioning and memory extinction. The model is tailored to the existing anatomical data and involves two circuit motives of central functional importance. It employs plastic synaptic connections between Kenyon cells and mushroom body output neurons (MBONs) in separate and mutually inhibiting appetitive and aversive learning pathways. Recurrent modulation of plasticity through projections from MBONs to reinforcement-mediating dopaminergic neurons implements a simple reward prediction mechanism. A distinct set of four MBONs encodes odor valence and predicts behavioral model output. Subjecting our model to learning and extinction protocols reproduced experimental results from recent behavioral and imaging studies. Simulating the experimental blocking of synaptic output of individual neurons or neuron groups in the model circuit confirmed experimental results and allowed formulation of testable predictions. In the temporal domain, our model achieves rapid learning with a step-like increase in the encoded odor value after a single pairing of the conditioned stimulus with a reward or punishment, facilitating single-trial learning.
31P NMR Spectroscopy Demonstrates Large Amounts of Phosphohistidine in Mammalian Cells
Authors: Makwana Mehul V. , van Meurs Sandra , Hounslow Andrea M. , Williamson Mike P. , Jackson Richard F. W. , Muimo Richmond
Published: December 2020

Protein phosphorylation plays a key role in many cellular processes but there is presently no accurate information or reliable procedure to determine the relative abundance of many phosphoamino acids in cells. At pH ≤ 8, phosphohistidine is unstable compared to the extensively studied phosphoserine, phosphothreonine and phosphotyrosine. This study reports the absolute quantitative analysis of histidine phosphorylation of proteins from a human bronchial epithelial cell (16HBE14o-) lysate using31P NMR spectroscopic analysis. The method was designed to minimize loss of the phosphohistidine phosphoryl group. Phosphohistidine was determined on average to be approximately one third as abundant as phosphoserine and phosphothreonine combined (and thus roughly 20 times more abundant than phosphotyrosine). The amount of phosphohistidine, and phosphoserine/phosphothreonine per gram of protein from a cell lysate was determined to be 23 μmol/g and 68 μmol/g respectively. The amount of phosphohistidine, and phosphoserine/phosphothreonine per cell was determined to be 1.8 fmol/cell, and 5.8 fmol/cell respectively. After tryptic digest of proteins from the16HBE14o- cell lysate, the phosphohistidine signal was abolished and increasing phosphoserine/phosphothreonine signal was observed, which has implications for mass spectrometry investigations. The31P NMR spectroscopic analysis not only highlights the abundance of phosphohistidine, which likely reflects its importance in mammalian cells, but also provides a way of measuring and comparing levels of phosphorylated amino acids in cells.
Seizure localisation with attention-based graph neural networks
Authors: Grattarola Daniele , Livi Lorenzo , Alippi Cesare , Wennberg Richard , Valiante Taufik A.
Published: December 2020

In this paper, we introduce a machine learning methodology for localising the seizure onset zone in subjects with epilepsy. We represent brain states as functional networks obtained from intracranial electroen-cephalography recordings, using correlation and the phase locking value to quantify the coupling between different brain areas.

Our method is based on graph neural networks (GNNs) and the attention mechanism, two of the most significant advances in artificial intelligence in recent years. Specifically, we train a GNN to distinguish between functional networks associated with interictal and ictal phases. The GNN is equipped with an attention-based layer that automatically learns to identify those regions of the brain (associated with individual electrodes) that are most important for a correct classification. The localisation of these regions does not require any prior information regarding the seizure onset zone.

We show that the regions of interest identified by the GNN strongly correlate with the localisation of the seizure onset zone reported by electroencephalographers. We report results both for human patients and for simulators of brain activity. We also show that our GNN exhibits uncertainty on those patients for which the clinical localisation was unsuccessful, highlighting the robustness of the proposed approach.
Fossils improve phylogenetic analyses of morphological characters
Authors: Koch Nicolás Mongiardino , Garwood Russell J. , Parry Luke A.
Published: December 2020

Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help elucidate macroevolutionary patterns and processes, such as ancestral states and diversification dynamics. However, the effect fossils have on phylogenetic inference from morphological data remains controversial. Previous studies have highlighted their strong impact on topologies inferred from empirical data, but have not demonstrated that they improve accuracy. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here we employ a simulation approach to explore how fossil sampling and missing data affect tree reconstruction across a range of inference methods. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses which simultaneously infer tree topology and divergence times outperform all other methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their unique morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.
Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer
Authors: Obr Martin , Ricana Clifton L. , Nikulin Nadia , Feathers Jon-Philip R. , Klanschnig Marco , Thader Andreas , Johnson Marc C. , Vogt Volker M. , Schur Florian K.M. , Dick Robert A.
Published: December 2020

Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 was ∼100-fold more potent at promoting RSV mature CA assembly than observed for HIV-1 and removal of IP6in vivoreduced infectivity by 100-fold. By cryo-electron tomography and subtomogram averaging, mature virus-like particles (VLPs) showed an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 had opposing effects on CAin vitroassembly, inducing formation of T=1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles revealed that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.