bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear Reconfiguration of Network Edges, Topology and Information Content During an Artifical Learning Task
Authors: Shine James M. , Li Mike , Koyejo Oluwasanmi , Fulcher Ben , Lizier Joseph T.
Published: October 2020

Network neuroscience has yielded crucial insights into the systems-level organisation of the brain, however the indirect nature of neuroimaging recordings has rendered the discovery of generative mechanisms for a given function inherently challenging. In parallel, neural network machine-learning models have exhibited breakthrough performance in tackling a range of complex problems, however the principles that govern learning-induced modifications to network structure remain poorly understood, in part due to a lack of analytic tools to quantify the dynamics of network structure. While the question of how network reconfiguration supports learning is mirrored in machine learning and network neuroscience, the different contexts of these fields provides a timely opportunity to bring them together synergistically to investigate the problem. Here we combine these two approaches to reveal connections between the brain’s network structure and the emerging network structure of an artificial neural network. Specifically, we train a shallow, feedforward neural network to classify handwritten digits and then used a combination of systems neuroscience and information theoretic tools to perform ‘virtual brain analytics’ on the resultant edge weights and activity patterns of each node. We identify three distinct phases of network reconfiguration across learning, each of which are characterised by unique topological and information-theoretic signatures. Each phase involves aligning the connections of the neural network with patterns of information contained in the input dataset or preceding layers (as relevant). We also observe a process of low-dimensional category separation in the network as a function of learning. Our results offer a systems-level perspective of how artificial neural networks function – in terms of multi-stage reorganization of edge weights and activity patterns to effectively exploit the information content of input data during edge-weight training – while simultaneously enriching our understanding of the methods used by systems neuroscience.
Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020
Authors: Dyrdak Robert , Hodcroft Emma B. , Wahlund Martina , Neher Richard A. , Albert Jan
Published: October 2020

Objectives

The four seasonal coronaviruses 229E, NL63, OC43, and HKU1 are frequent causes of respiratory infections and show annual and seasonal variation. Increased understanding about these patterns could be informative about the epidemiology of SARS-CoV-2.

Methods

Results from PCR diagnostics for the seasonal coronaviruses, and other respiratory viruses, were obtained for 55,190 clinical samples analysed at the Karolinska University Hospital, Stockholm, Sweden, between 14 September 2009 and 2 April 2020.

Results

Seasonal coronaviruses were detected in 2,130 samples (3.9%) and constituted 8.1% of all virus detections. OC43 was most commonly detected (28.4% of detections), followed by NL63 (24.0%), HKU1 (17.6%), and 229E (15.3%). The overall fraction of positive samples was similar between seasons, but at species level there were distinct biennial alternating peak seasons for the Alphacoronaviruses, 229E and NL63, and the Betacoronaviruses, OC43 and HKU1, respectively. The Betacoronaviruses peaked earlier in the winter season (Dec-Jan) than the Alphacoronaviruses (Feb-Mar). Coronaviruses were detected across all ages, but diagnostics were more frequently requested for paediatric patients than adults and the elderly. OC43 and 229E incidence was relatively constant across age strata, while that of NL63 and HKU1 decreased with age.

Conclusions

Both the Alphacoronaviruses and Betacoronaviruses showed alternating biennial winter incidence peaks, which suggests some type of immune mediated interaction. Symptomatic reinfections in adults and the elderly appear relatively common. Both findings may be of relevance for the epidemiology of SARS-CoV-2.
COVID-19 Pandemic in University Hospital: Is There an Effect on The Medical Interns?
Authors: Lim WeiHonn , Teoh Li Ying , Seevalingam Kanesh Kumaran A/L , Kuppusamy Shanggar
Published: October 2020

Introduction

Coronavirus Disease 2019 (COVID-19) pandemic has disrupted the current healthcare system and carries a major impact to the healthcare workers (HCW). University Malaya Medical Centre (UMMC) has been selected as one of the centres in managing COVID-19 cases in Malaysia. Many HCW including the medical interns, are directly or indirectly involved in the management.

Methods

This is a cross-sectional, pilot study to determine the impact of the pandemic on UMMC medical interns. A survey which comprises 37-items was used. Data are analysed by Ordinal Logistic Regression Analysis.

Results

Our study shows that medical interns are tired (p = 0.014), starving (p = 0.004), have inadequate exercises (p = 0.004) and burdened with heavy workload (p=0.023) during pandemic period. Many are depressed (p = 0.043), scared to work (p = 0.03), and worried of getting infected (p < 0.05). Some quarrel with their colleagues (p < 0.05), losing contact with friends (p = 0.022) and feel that it will be beneficial to have a peer support group (p = 0.027).

Conclusion

In summary, the impact of COVID-19 amongst medical interns is significant and their overall well-being should be protected without jeopardising their training.
Studying bone marrow-derived macrophages needs to consider the influence of cells apart from macrophage, especially the selection of markers
Authors: Chu Chenyu , Rung Shengan , Wang Yufei , Qu Yili , Man Yi
Published: October 2020

Culturing macrophage in vitro is an important means to understand its reaction towards co-culture substances. However, the source of macrophages can be either purchased from specific cell line or extracted from bone marrow as differentiated macrophages. In order to assure the precision, when adopting extracted primary cell, screening in advance will be prominent before any processes to avoid results reserving that of non-macrophages. Here, we perform single-cell sequencing on open wound of skin in mice and focusing on the secreted proteins and surface markers related to traditional macrophage phenotypes (M1/M2) to ensure the importance of screening. The expression of CAMP when macrophages fight against candida albicans is another target to see its relationship with current classification. And results showed that identifying its phenotype without screening macrophages will far from the exact situation, and the expression of CAMP cannot be carried out by the traditional M1 and M2 macrophage. Thus, determining phenotype of macrophages based on function would be a promising way.
A test of altitude-related variation in aerobic metabolism of Andean birds
Authors: Gutierrez-Pinto Natalia , Londoño Gustavo A. , Chappell Mark A. , Storz Jay F.
Published: October 2020

Endotherms at high altitude face the combined challenges of cold and hypoxia. Cold increases thermoregulatory costs, and hypoxia may limit both thermogenesis and aerobic exercise capacity. Consequently, in comparisons between closely related highland and lowland taxa, we might expect to observe consistent differences in basal metabolism (BMR), maximal metabolism (MMR), and aerobic scope. Broad-scale comparative studies of birds reveal no association between BMR and native elevation, and altitude effects on MMR have not been investigated. We tested for altitude-related variation in aerobic metabolism in 10 Andean passerines representing five pairs of closely related species with contrasting elevational ranges. Mass-corrected BMR and MMR were significantly higher in most highland species relative to their lowland counterparts, but there was no uniform elevational trend across all pairs of species.

Summary statement

We tested for altitude-related variation in aerobic metabolism in species pairs with contrasting elevational ranges. Metabolic rates were significantly higher in most highland species but there was no uniform elevational trend.
Production of the infant formula ingredient 1,3-olein-2-palmitin in Arabidopsis seeds
Authors: van Erp Harrie , Bryant Fiona M , Martin-Moreno Jose , Eastmond Peter J
Published: October 2020

In human milk fat, palmitic acid (16:0) is esterified to the middle (sn-2 or β) position on the glycerol backbone and oleic acid (18:1) predominantly to the outer positions, giving the triacylglycerol (TG) a distinctive stereoisomeric structure that is believed to assist nutrient absorption in the infant gut. However, the fat used in most infant formulas is derived from plants, which preferentially esterify 16:0 to the outer positions. We have previously showed that the metabolism of the model oilseedArabidopsis thalianacan be engineered to incorporate 16:0 into the middle position of TG. However, the fatty acyl composition of Arabidopsis seed TG does not mimic human milk, which is rich in both 16:0 and 18:1 and is defined by the high abundance of the TG molecular species 1,3-olein-2-palmitin (OPO). Here we have constructed an Arabidopsisfatty acid biosynthesis 1-1 fatty acid desaturase 2 fatty acid elongase 1mutant with around 20% 16:0 and ~70% 18:1 in its seeds and we have engineered it to esterify more than 80% of the 16:0 to the middle position of TG, using heterologous expression of the human lysophosphatidic acid acyltransferase isoform AGPAT1, combined with suppression of LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE 2 and PHOSPHATIDYLCHOLINE:DIACYLGLYCEROL CHOLINEPHOSPHOTRANSFERASE. Our data suggest that oilseeds can be engineered to produce TG that is rich in OPO, which is an important structured fat ingredient used in infant formulas.
Molecular Parallelisms and Divergences Between Human and Canine Cancers Would a dog be an appropriate experimental model for human cancers?
Authors: Ambreen Sadaf , Guanhan Li , Zhao Binbin , Bao Gang , Song Yiwen , Lin Degui , Wu Dafei , Hou Yali , Lu Xuemei
Published: October 2020

Canine mammary cancer is poorly characterized at the genomic level. Dog really can be an appropriate experimental model for human cancers from the genomic and evolutionary perspective or not? Here, we perform a cross-species cancer genomics analysis, independent evolution of cancer from normal tissues, which provide us an excellent opportunity to address an evolutionary perspective of cancer. As, evolutionary theories are critical for understanding tumorigenesis at the level of species as well as at the level of cells and tissues, for the development of effective therapies. Analysis of canine mammary cancer reveals a diversity of histological types as compare to human breast cancer. Our systematic analysis of 24 canine mammary tumors with whole-genome sequences, reveals 185 protein-coding cancer genes carried exonic mutations. Cross-species comparative analysis of 1080 human breast cancers identifies higher median mutation frequency in human breast cancer and canine mammary cancer shows lower across exonic regions (2.67 and 0.187 average no. of mutations per tumor per megabase (Mb), respectively). A comparison of somatic mutations in thePIK3CAgene, reveals common recurrence of the conserved mutations, in both species. However, the Ka/Ks ratio in the humanPIK3CAgene 2.37 is higher and 1.43 in dogs is lower. To address the mutation accumulation and antagonistic pleiotropy theory, we investigated Ka/Ks value 237 aging-related genes from human and canine, the aging-related genes do not show selection in canine mammary cancer. It demonstrates new aspects of cancer genes that are evolving in different species instantaneously. These findings may suggest, the same organs in different mammals impose different selective pressures on the same set of genes in cancer. In both species, some genes may experience strong selective pressures, but do not converge genetically or the conserved genes do not show the same selection pressure in both species. However, human breast cancer shows transcriptomic similarity with canine mammary carcinoma but the other subtypes are quite different. We found canine mammary tumor can be used as a model for inter and intra-tumor heterogeneity. These findings provided insight into mammary cancer across species and possessed potential clinical significance. Collectively, these studies suggest a convergence of some genetic changes in mammary cancer between species but also distinctly different paths to tumorigenesis.
High Throughput RNA Sequencing of Germ-Free Mouse Retina Reveals Metabolic Pathways Involved in the Gut-Retina Axis
Authors: Nadeem Urooba , Xie Bingqing , Movahedan Asadolah , D’Souza Mark , Barba Hugo , Deng Nini , Leone Vanessa A. , Chang Eugene , Sulakhe Dinanath , Skondra Dimitra
Published: October 2020

Background and aims

Connections between the gut microbiome and retinal diseases such as age-related macular degeneration (AMD), diabetic retinopathy (DR), retinopathy of prematurity (ROP), and primary open-angle glaucoma (POAG) are recently being established. Communication between the gut microbiome and retina, referred to as the gut-retina axis, has been proposed; however, the biologic pathways and mediators involved in the interactions have not yet been elucidated. Using high-throughput RNA sequencing (RNA-seq) of whole retinas, we compare the retinal transcriptome from germ-free (GF) and specific pathogen-free (SPF) mice to investigate the effects of the gut-microbiome on both retinal gene expression and biologic pathways.

Methods

RNA was extracted from whole retinas of GF and SPF mice (four animals per group) and cDNA libraries were created. RNA-seq was performed on NovaSEQ6000 using the paired-end method. After preprocessing the RNA-seq data, gene expression value was calculated by count per million (CPM). The differentially expressed genes (DEGs) were identified with the limma package from Bioconductor on the expression data. Functional enrichment and protein-protein interaction STRING protein-protein association network analyses were created for the differentially expressed genes (DEGs).

Results

RNA-sequencing reveals a cohort of 396 DEGs, of which, 173 are upregulated and 223 are downregulated in GF mouse retina. Enrichment analysis reveals that the DEGs are involved in glucocorticoid effects, transcription factor binding, cytoskeletal stability, lipid metabolism, and mitogen-activated protein kinase (MAPK). Multiple biologic pathways, including obesity/metabolic syndrome, longevity, insulin-like growth factor (IGF) signaling pathway, vascular endothelial growth factor (VEGF), hypoxia-inducible factor(HIF)-1 transcription pathway, and 5’ AMP-activated protein kinase(AMPK) signaling pathway are affected in the GF retinas. PPARG1a (PGC1a) gene is involved in 13 of the 35 significantly modulated pathways. Proteins with the greatest number of interactions in the PPI are E1A binding protein P300(EP300), forkhead box O3(FOXO3), and PGC1a.

Conclusions

To our knowledge, this is the first study demonstrating the involvement of the gut microbiome in driving the retinal transcriptome, providing evidence for the presence of a gut-retina axis. Future studies are needed to define the precise role of the gut-retina axis in the pathogenesis of retinal diseases.
A novel algorithm to accurately classify metagenomic sequences
Authors: Saha Subrata , Wang Zigeng , Rajasekaran Sanguthevar
Published: October 2020

Widespread availability of next-generation sequencing (NGS) technologies has prompted a recent surge in interest in the microbiome. As a consequence, metagenomics is a fast growing field in bioinformatics and computational biology. An important problem in analyzing metagenomic sequenced data is to identify the microbes present in the sample and figure out their relative abundances. In this article we propose a highly efficient algorithm dubbed as “Hybrid Metagenomic Sequence Classifier” (HMSC) to accurately detect microbes and their relative abundances in a metagenomic sample. The algorithmic approach is fundamentally different from other state-of-the-art algorithms currently existing in this domain. HMSC judiciously exploits both alignment-free and alignment-based approaches to accurately characterize metagenomic sequenced data. To demonstrate the effectiveness of HMSC we used 8 metagenomic sequencing datasets (2mockand 6in silicobacterial communities) produced by 3 different sequencing technologies (e.g., HiSeq, MiSeq, and NovaSeq) with realistic error models and abundance distribution. Rigorous experimental evaluations show that HMSC is indeed an effective, scalable, and efficient algorithm compared to the other state-of-the-art methods in terms of accuracy, memory, and runtime.

Availability of data and materials

The implementations and the datasets we used are freely available for non-commercial purposes. They can be downloaded from:https://drive.google.com/drive/folders/132k5E5xqpkw7olFjzYwjWNjyHFrqJITe?usp=sharing
Individual small in-stream barriers contribute little to strong local population genetic structure five strictly aquatic macroinvertebrate taxa
Authors: Weiss Martina , Weigand Hannah , Leese Florian
Published: October 2020

Water flow in river networks is frequently regulated by man-made in-stream barriers. These obstacles can hinder dispersal of aquatic organisms and isolate populations leading to the loss of genetic diversity. Although millions of small in-stream barriers exist worldwide, such as weirs below 2 m or tunnels and pipes, their impact on the dispersal of macroinvertebrates with strictly aquatic life cycles is unclear. We therefore assessed the effects of such barriers on the population structure and effective dispersal of five macroinvertebrate species with strictly aquatic life cycles: the amphipod crustacean Gammarus fossarum (clade 11), three snail species of the Ancylus fluviatilis species complex and the flatworm Dugesia gonocephala. We studied populations at nine weirs and eight culverts (3 pipes, 5 tunnels), built 33-109 years ago, in the heavily fragmented catchment of the river Ruhr (Sauerland, Germany). To assess fragmentation and barrier effects, we generated genome-wide SNP data using ddRAD sequencing and evaluated clustering, differentiation between populations up- and downstream of each barrier and effective migration rates among sites and across barriers. Additionally, we applied population genomic simulations to assess expected differentiation patterns under different gene flow scenarios. Our data show that populations of all species are highly isolated at regional and local scales within few kilometres. While the regional population structure likely results from historical processes, the strong local differentiation suggests that contemporary dispersal barriers exist. However, we identified significant barrier effects only for pipes (for A. fluviatilis II and III) and few larger weirs (>1.3 m; for D. gonocephala). Therefore our data suggest that most small in-stream barriers can probably be overcome by all studied taxa frequently enough to prevent fragmentation. Thus, the barriers leading to population isolation after few kilometres still need to be identified. Specifically, it remains to be tested if the strong local differentiation is a result of a cumulative effect of small barriers, or if e.g. larger in-stream barriers, land use, chemical pollution, urbanisation, or a combination of these factors impede gene flow.
Highly responsive single-fluorophore indicator to explore lactate dynamics in high calcium environments
Authors: Galaz A. , Sandoval PY. , Soto-Ojeda I. , Hertenstein H. , Schweizer J. , Schirmeier S. , Barros L.F , San Martín A.
Published: October 2020

Lactate is an energy substrate and intercellular signaling molecule with multiple bodily functions. Lactate has physiological roles in neurogenesis, axon integrity, memory consolidation, immune response, exercise, adipose tissue lipolysis, etc, and is involved in inflammation, cancer and neurodegeneration. The FRET lactate indicator Laconic has been instrumental in the discovery of mechanisms involved in neurometabolic coupling, and has advanced the understanding of lactate transport, glycolysis and mitochondrial physiology. However, the low fluorescent response and the complex saturation kinetics of Laconic limit its use for high-throughput screening and quantitation. Using the bacterial periplasmic binding protein TTHA0766 fromThermus thermophilus, we have now developed the first single-fluorophore indicator for lactate. The sensor exhibited an intensiometric fluorescence increase of ΔF/F03.0 and a single binding site with a KDof 293 μM. The fluorescence is not affected by other monocarboxylates or pH. However, it is sensitive to Ca2+in the nanomolar range. Targeting of the sensor to the endoplasmic reticulum revealed that this organelle presents a high permeability for lactate. The functionality of the sensor in living tissue is demonstrated in the brain ofDrosophila melanogasterlarvae. This indicator, which we have termed CanlonicSF, is well suited to explore lactate dynamics in environments with micromolar Ca2+or higher, such as the endoplasmic reticulum and the extracellular space.
Establishment of a new sex-determining allele driven by sexually antagonistic selection
Authors: Sakamoto T. , Innan H.
Published: October 2020

Some species undergo frequent turnovers of sex-determining locus, rather than having stable diverged sex chromosomes. In such species, how often turnover occurs is a fundamental evolutionary question. We model the process with considering a linked locus under sexually antagonistic selection. The entire process of a turnover may be divided into two phases, which are referred to as the stochastic and deterministic phases. The stochastic phase is when a new sex-determining allele just arises and is still rare and random genetic drift plays an important role. In the deterministic phase, the new allele further increases in frequency by positive selection. The theoretical results currently available are for the deterministic phase, which demonstrated that a turnover of a newly arisen sex determining locus could benefit from selection at a linked locus under sexually antagonistic selection, by assuming that sexually antagonistic selection works in a form of balancing selection. In this work, we provide a comprehensive theoretical description of the entire process from the stochastic phase to the deterministic phase. In addition to balancing selection, we explore several other modes of selection on the linked locus. Our theory allows us make a quantitative argument on the rate of turnover and the effect of the mode of selection at the linked locus. We also performed simulations to explore the pattern of polymorphism around the new sex determining locus. We find that the pattern of polymorphism is informative to infer how selection worked through the turnover process.
Spatial fingerprinting: horizontal fusion of multi-dimensional bio-tracers as solution to global food provenance problems
Authors: Cazelles Kevin , Zemlak Tyler , Gutgesell Marie , Myles-Gonzalez Emelia , Hanner Robert , McCann Kevin S.
Published: October 2020

Building the capacity of efficiently determining the provenance of food products represents a crucial step towards the sustainability of the global food system. Whether it is for enforcing existing egislation or providing reliable information to consumers, technologies to verify geographical origin of food are being actively developed. Biological tracers (bio-tracers) such as DNA and stable isotopes have recently demonstrated their potential for determining provenance. Here we show that the data fusion of bio-tracers is a very powerful technique for geographical provenance discrimination. Based on 90 individuals of Sockeye salmon that originate from 3 different areas for which we measured 17 bio-tracers, we demonstrate that increasing the combined bio-tracers results in stronger the discriminatory power. The generality of our results are mathematically demonstrated under simplifying assumptions and numerically confirmed in our case study using three commonly used supervised learning techniques.
Morphine alleviates pain after heart cryoinjury in zebrafish without impeding regeneration
Authors: Lelek Sara , Simões Mariana Guedes , Hu Bo , Alameldeen Ahmed M.A. , Czajkowski Maciej T. , Meyer Alexander M. , Ferrara Fabienne , Junker Jan Philipp , Panáková Daniela
Published: October 2020

Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish, similarly to higher vertebrates, also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not, however, take into account the adverse effects including pain that may potentially arise from these methodologies. Here, we assess the effect of two analgesics, lidocaine and morphine, followed after heart cryoinjury in zebrafish. Monitoring swimming behavior together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescentin situhybridization technology, we show morphine, but not lidocaine, significantly improves animal welfare 6 hours post-cryoinjury, without impairing the heart regeneration process. Altogether, we propose morphine to be considered as the analgesic of choice to reduce post-surgical pain in adult zebrafish.

Highlights

Cryoinury could be considered as a potential noxious stimulus in adult zebrafish.

Morphine but not lidocaine treatment effectively alleviates noxious effects post-cryoinjury.

Lidocaine treatment delays heart repair and regeneration.

6 hours Morphine treatment after cryoinjury does not impede heart regeneration.
Dwarf open reading frame (DWORF) peptide is a direct activator of the sarcoplasmic reticulum calcium pump SERCA
Authors: Fisher M’Lynn E. , Bovo Elisa , Cho Ellen E. , Pribadi Marsha P. , Dalton Michael P. , Lemieux M. Joanne , Rathod Nishadh , Aguayo-Ortiz Rodrigo , Espinoza-Fonseca L. Michel , Robia Seth L. , Zima Aleksey V. , Young Howard S.
Published: October 2020

The cardiac sarcoplasmic reticulum calcium pump, SERCA, sequesters calcium in the sarco-endoplasmic reticulum (SR/ER) and plays a critical role in the contraction-relaxation cycle of the heart. A well-known regulator of SERCA in cardiac muscle is phospholamban (PLN), which interacts with the pump and reduces its apparent calcium affinity. A newly discovered SERCA regulatory subunit in cardiac muscle, dwarf open reading frame (DWORF), has added a new level of SERCA regulation. In this report, we modeled the structure of DWORF and evaluated it using molecular dynamics simulations. DWORF structure was modeled as a discontinuous helix with an unwound region at Pro15. This model orients an N-terminal amphipathic helix along the membrane surface and leaves a relatively short C-terminal transmembrane helix. We determined the functional regulation of SERCA by DWORF using a membrane reconstitution system. Surprisingly, we observed that DWORF directly activated SERCA by increasing its turnover rate. Furthermore, in-cell imaging of calcium dynamics demonstrated that DWORF increased SERCA-dependent ER calcium load, calcium reuptake rate, and spontaneous calcium release. Together, these functional assays suggest opposing effects of DWORF and PLN on SERCA function. The results agree with fluorescence resonance energy transfer experiments, which revealed changes in the affinity of DWORF for SERCA at low versus high cytosolic calcium concentrations. We found that DWORF has a higher affinity for SERCA in the presence of calcium, while PLN had the opposite behavior, a higher affinity for SERCA in low calcium. We propose a new mechanism for DWORF regulation of cardiac calcium handling in which DWORF directly enhances SERCA turnover by stabilizing the conformations of SERCA that predominate during elevated cytosolic calcium.
Identification of Influential Variants in Significant Aggregate Rare Variant Tests
Authors: Blumhagen Rachel Z. , Schwartz David A. , Langefeld Carl D. , Fingerlin Tasha E.
Published: October 2020

Introduction

Studies that examine the role of rare variants in both simple and complex disease are increasingly common. Though the usual approach of testing rare variants in aggregate sets is more powerful than testing individual variants, it is of interest to identify the variants that are plausible drivers of the association. We present a novel method for prioritization of rare variants after a significant aggregate test by quantifying the influence of the variant on the aggregate test of association.

Methods

In addition to providing a measure used to rank variants, we use outlier detection methods to present the computationally efficientRare Variant InfluentialFilteringTool (RIFT) to identify a subset of variants that influence the disease association. We evaluated several outlier detection methods that vary based on the underlying variance measure: interquartile range (Tukey fences), median absolute deviation and standard deviation. We performed 1000 simulations for 50 regions of size 3kb and compared the true and false positive rates. We compared RIFT using the Inner Tukey to two existing methods: adaptive combination of p-values (ADA) and a Bayesian hierarchical model (BeviMed). Finally, we applied this method to data from our targeted resequencing study in idiopathic pulmonary fibrosis (IPF).

Results

All outlier detection methods observed higher sensitivity to detect uncommon variants (0.001 < MAF > 0.03) compared to very rare variants (MAF < 0.001). For uncommon variants, RIFT had a lower median false positive rate compared to the ADA. ADA and RIFT had significantly higher true positive rates than that observed for BeviMed. When applied to two regions found previously associated with IPF including 100 rare variants, we identified six polymorphisms with the greatest evidence for influencing the association with IPF.

Discussion

In summary, RIFT has a high true positive rate while maintaining a low false positive rate for identifying polymorphisms influencing rare variant association tests. This work provides an approach to obtain greater resolution of the rare variant signals within significant aggregate sets; this information can provide an objective measure to prioritize variants for follow-up experimental studies and insight into the biological pathways involved.
Segmentation and analysis of mother machine data: SAM
Authors: Banerjee Deb Sankar , Stephenson Godwin , Das Suman G.
Published: October 2020

Time-lapse imaging of bacteria growing in micro-channels in a controlled environment has been instrumental in studying the single cell dynamics of bacterial growth. This kind of a microfluidic setup with growth chambers is popularly known asmother machine[1]. In a typical experiment with such a set-up, bacterial growth can be studied for numerous generations with high resolution and temporal precision using image processing. However, as in any other experiment involving imaging, the image data from a typical mother machine experiment has considerable intensity fluctuations, cell intrusion, cell overlapping, filamentation etc. The large amount of data produced in such experiments makes it hard for manual analysis and correction of such unwanted aberrations. We have developed a modular code for segmentation and analysis of mother machine data (SAM) for rod shaped bacteria where we can detect such aberrations and correctly treat them without manual supervision. We track cumulative cell size and use an adaptive segmentation method to avoid faulty detection of cell division. SAM is currently written and compiled using MATLAB. It is fast (∼ 15min/GBof image) and can be efficiently coupled with shell scripting to process large amount of data with systematic creation of output file structures and graphical results. It has been tested for many different experimental data and is publicly available in Github.
Emerging strains of watermelon mosaic virus in Southeastern France: model-based estimation of the dates and places of introduction
Authors: Roques L , Desbiez C , Berthier K , Soubeyrand S , Walker E , Klein E K , Garnier J , Moury B , Papaïx J
Published: October 2020

Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction-diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genusPotyvirus, familyPotyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.
Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae
Authors: Jacobs-Palmer Emily , Gallego Ramón , Cribari Kelly , Keller Abigail , Kelly Ryan P.
Published: October 2020

Harmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. We track trends of presence and abundance in a series of water samples across nearly two years. We find putative harmful algal sequences in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genusPseudo-nitzschia(family Bacillariaceae), as well as multiple harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the saxitoxin-producing genusAlexandrium(family Gonyaulacaceae), two variants from the karlotoxin-producing genusKarlodinium(family Kareniaceae), and one variant from the parasitic genusHematodinium(family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which these species are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of harmful algae, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) provides a tool for monitoring and management moving forward.
Rational Tuning of CAR Tonic Signaling Yields Superior T-Cell Therapy for Cancer
Authors: Chen Ximin , Khericha Mobina , Lakhani Aliya , Meng Xiangzhi , Salvestrini Emma , Chen Laurence C. , Shafer Amanda , Alag Anya , Ding Yunfeng , Nicolaou Demetri , Park Junyoung O. , Chen Yvonne Y.
Published: October 2020

Chimeric antigen receptors (CARs) are modular proteins capable of redirecting immune cells toward a wide variety of disease-associated antigens. Here, we explore the effects of CAR protein sequence and structure on CAR-T cell function. Based on the empirical observation that CD20 CARs with similar sequences exhibit divergent tonic-signaling and anti-tumor activities, we devised engineering strategies that aimed to improve CAR-T cell function by tuning the intensity of tonic signaling. We found that CARs designed to exhibit low but non-zero levels of tonic signaling show robust effector function upon antigen stimulation while avoiding premature functional exhaustion by CAR-T cells. Through alterations of the CAR’s ligand-binding domain and overall protein conformation, we generated CD20 CAR variants that outperform the CD19 CAR in mouse models of human lymphoma. We further demonstrate that rational modification of protein confirmation can be generalized to improve GD2 CAR-T cell efficacy against neuroblastoma. These findings point to tonic signaling and basal T-cell activation as informative parameters to guide the rational design of next-generation CARs for cancer therapy.
Seroprevalence of SARS-COV-2 Antibodies in Scottish Healthcare Workers
Authors: Abo-Leyah Hani , Gallant Stephanie , Cassidy Diane , Giam Yan Hui , Killick Justin , Marshall Beth , Hay Gordon , Pembridge Thomas , Strachan Rachel , Gallant Natalie , Parcell Benjamin J , George Jacob , Furrie Elizabeth , Chalmers James D
Published: October 2020

Introduction

Healthcare workers are believed to be at increased risk of SARS-CoV-2 infection. The extent of that increased risk compared to the general population and the groups most at risk have not been extensively studied.

Methods

A prospective observational study of health and social care workers in NHS Tayside (Scotland, UK) from May to September 2020. The Siemens SARS-CoV-2 total antibody assay was used to establish seroprevalence in this cohort. Patients provided clinical information including demographics and workplace information. Controls, matched for age and sex to the general Tayside population, were studied for comparison.

Results

A total of 2062 health and social care workers were recruited for this study. The participants were predominantly female (81.7%) and 95.2% were white. 299 healthcare workers had a positive antibody test (14.5%). 11 out of 231 control sera tested positive (4.8%). Healthcare workers therefore had an increased likelihood of a positive test (odds ratio 3.4 95% CI 1.85-6.16, p<0.0001). Dentists, healthcare assistants and porters were the job roles most likely to test positive. Those working in front-line roles with COVID-19 patients were more likely to test positive (17.4% vs. 13.4%, p=0.02). 97.1% of patients who had previously tested positive for SARS-CoV-2 by RT-PCR had positive antibodies, compared to 11.8% of individuals with a symptomatic illness who had tested negative. Anosmia was the symptom most associated with the presence of detectable antibodies.

Conclusion

In this study, healthcare workers were three times more likely to test positive for SARS-CoV-2 than the general population. The seroprevalence data in different populations identified in this study will be useful to protect healthcare staff during future waves of the pandemic.
Single Cell Analysis of Regions of Interest (SCARI) using a novel photoswitchable tag
Authors: van der Leun Anne M. , Hoekstra Mirjam E. , Reinalda Luuk , Scheele Colinda L.G.J. , Toebes Mireille , van de Graaff Michel J. , Li Hanjie , Bercovich Akhiad , Lubling Yaniv , David Eyal , Thommen Daniela S. , Tanay Amos , van Rheenen Jacco , Amit Ido , van Kasteren Sander I. , Schumacher Ton N.
Published: October 2020

The functional activity and differentiation potential of cells is determined by their interaction with surrounding cells. Approaches that allow the unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a trade-off between spatial resolution and cell profiling depth. Here, we developed a photoswitch-based technology that allows the isolation and in-depth analysis of live cells from regions of interest in complexex vivosystems, including human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran)-cage coupled to nanobodies allowed photoswitching of cells in areas of interest with low-intensity violet light and without detectable phototoxicity. Single cell RNA sequencing of spatially defined CD8+T cells was used to exemplify the feasibility of identifying location-dependent cell states at the single cell level. Finally, we demonstrate the efficient labeling and photoswitching of cells in live primary human tumor tissue. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples.
Lung macrophages mediate helminth resistance through differential activation of recruited monocyte-derived alveolar macrophages and arginine depletion
Authors: Chen Fei , El-Naccache Darine W. , Ponessa John J. , Lemenze Alexander , Espinosa Vanessa , Wu Wenhui , Lothstein Katherine , Jin Linhua , Antao Olivia , Weinstein Jason S. , Damani-Yokota Payal , Khanna Kamal , Murray Peter , Rivera Amariliz , Siracusa Mark C. , Gause William C.
Published: October 2020

Macrophages are known to mediate anti-helminth responses, but it remains uncertain which subsets are involved or how macrophages actually kill helminths. Here we show rapid monocyte recruitment to the lung after infection with the nematode parasite,Nippostrongylus brasiliensis. In this inflamed tissue microenvironment these monocytes differentiate into an alveolar-like macrophage (AM) phenotype, expressing both Siglec-F and CD11c, surround invading parasitic larvae and preferentially kill parasites in vitro. Monocyte-derived AMs (Mo-AMs) express type 2-associated markers and show distinct remodeling of the chromatin landscape relative to tissue-derived AMs. In particular, they express high amounts of Arg1 (arginase-1), which we demonstrate mediates helminth killing through L-arginine depletion. These studies indicate that recruited monocytes are selectively programmed in the pulmonary environment to express AM markers and an anti-helminth phenotype.
Unsupervised cellular phenotypic hierarchy enables spatial intratumor heterogeneity characterization, recurrence-associated microdomains discovery, and harnesses network biology from hyperplexed in-situ fluorescence images of colorectal carcinoma
Authors: Furman Samantha A. , Stern Andrew M. , Uttam Shikhar , Taylor D. Lansing , Pullara Filippo , Chennubhotla S. Chakra
Published: October 2020

LEAPH is an unsupervised machinelearningalgorithm for characterizing in situphenotypicheterogeneity in tissue samples. LEAPH builds a phenotypic hierarchy of cell types, cell states and their spatial configurations. The recursive modeling steps involve determining cell types with low-ranked mixtures of factor analyzers and optimizing cell states with spatial regularization. We applied LEAPH to hyperplexed (51 biomarkers) immunofluorescence images of colorectal carcinoma primary tumors (N=213). LEAPH, combined with pointwise mutual information (PMI), enables the discovery of phenotypically distinctmicrodomains, composed of spatially configured computational phenotypes. LEAPH identified a subset of microdomains visualized as the spatial configuration of recurrence-specific signaling networks whose intracellular and intercellular interactions support cancer stem cell maintenance and immunosuppression in the evolving tumor microenvironment. The LEAPH framework, when combined with microdomain discovery and microdomain-specific network biology, has the potential to provide insights into pathophysiological mechanisms, identify novel drug targets and inform therapeutic strategies for individual patients.
ScRNA-seq reveals tumor microenvironment remodeling induced by local intervention-based immunotherapy
Authors: Hoover Ashley R. , Liu Kaili , DeVette Christa I. , Krawic Jason R. , West Connor L. , Medcalf Delaney , Welm Alana L. , Sun Xiao-Hong , Hildebrand William H. , Chen Wei R.
Published: October 2020

Laser immunotherapy (LIT) combines local photothermal therapy (PTT), to disrupt tumor homeostasis and release tumor antigens, and an intratumorally administered immunostimulant, N-dihydrogalactochitosan (GC), to induce antitumor immune responses. We performed single-cell RNA sequencing on tumor-infiltrating leukocytes of MMTV-PyMT mouse mammary tumors to characterize LIT-induced myeloid and lymphoid compartment remodeling. Analysis of 49,380 single cell transcriptomes from different treatment groups revealed that proinflammatory IFNα, IFNγ, and TNFα cytokine signaling pathways were enriched in both lymphoid and myeloid cells isolated from LIT-treated tumors. The CD4+and CD8+T cells in LIT treated tumors resided in an activated state while immune cells in untreated and PTT-treated tumors remained in a neutral/resting state. Additionally, monocytes recruited into the LIT-treated tumors were driven towards proinflammatory M1-like macrophage phenotypes or monocyte-derived dendritic cells. Our results reveal that LIT prompts immunological remodeling of the tumor microenvironment by initiating broad proinflammatory responses to drive antitumor immunity.

STATEMENT OF SIGNIFICANCE

Transcriptome profiling of tumor infiltrating leukocytes revealed that localized laser immunotherapy (LIT) greatly enhanced antitumor T cell activity by promoting proinflammatory myeloid cell responses within the tumor microenvironment. This manuscript demonstrates that LIT broadly stimulates antitumor immunity and has great potential to synergize with current immunotherapies to increase their efficacy.
Cellular Anatomy of the Mouse Primary Motor Cortex
Authors: Muñoz-Castañeda Rodrigo , Zingg Brian , Matho Katherine S. , Wang Quanxin , Chen Xiaoyin , Foster Nicholas N. , Narasimhan Arun , Li Anan , Hirokawa Karla E. , Huo Bingxing , Bannerjee Samik , Korobkova Laura , Park Chris Sin , Park Young-Gyun , Bienkowski Michael S. , Chon Uree , Wheeler Diek W. , Li Xiangning , Wang Yun , Kelly Kathleen , An Xu , Attili Sarojini M. , Bowman Ian , Bludova Anastasiia , Cetin Ali , Ding Liya , Drewes Rhonda , D’Orazi Florence , Elowsky Corey , Fischer Stephan , Galbavy William , Gao Lei , Gillis Jesse , Groblewski Peter A. , Gou Lin , Hahn Joel D. , Hatfield Joshua T. , Hintiryan Houri , Huang Jason , Kondo Hideki , Kuang Xiuli , Lesnar Philip , Li Xu , Li Yaoyao , Lin Mengkuan , Liu Lijuan , Lo Darrick , Mizrachi Judith , Mok Stephanie , Naeemi Maitham , Nicovich Philip R. , Palaniswamy Ramesh , Palmer Jason , Qi Xiaoli , Shen Elise , Sun Yu-Chi , Tao Huizhong , Wakemen Wayne , Wang Yimin , Xie Peng , Yao Shenqin , Yuan Jin , Zhu Muye , Ng Lydia , Zhang Li I. , Lim Byung Kook , Hawrylycz Michael , Gong Hui , Gee James C. , Kim Yongsoo , Peng Hanchuan , Chuang Kwanghun , Yang X William , Luo Qingming , Mitra Partha P. , Zador Anthony M. , Zeng Hongkui , Ascoli Giorgio A. , Huang Z Josh , Osten Pavel , Harris Julie A. , Dong Hong-Wei
Published: October 2020

An essential step toward understanding brain function is to establish a cellular-resolution structural framework upon which multi-scale and multi-modal information spanning molecules, cells, circuits and systems can be integrated and interpreted. Here, through a collaborative effort from the Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based description of one brain structure - the primary motor cortex upper limb area (MOp-ul) of the mouse. Applying state-of-the-art labeling, imaging, computational, and neuroinformatics tools, we delineated the MOp-ul within the Mouse Brain 3D Common Coordinate Framework (CCF). We defined over two dozen MOp-ul projection neuron (PN) types by their anterograde targets; the spatial distribution of their somata defines 11 cortical sublayers, a significant refinement of the classic notion of cortical laminar organization. We further combine multiple complementary tracing methods (classic tract tracing, cell type-based anterograde, retrograde, and transsynaptic viral tracing, high-throughput BARseq, and complete single cell reconstruction) to systematically chart cell type-based MOp input-output streams. As PNs link distant brain regions at synapses as well as host cellular gene expression, our construction of a PN type resolution MOp-ul wiring diagram will facilitate an integrated analysis of motor control circuitry across the molecular, cellular, and systems levels. This work further provides a roadmap towards a cellular resolution description of mammalian brain architecture.