bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving generalization of deep learning models for diagnostic pathology by increasing variability in training data: experiments on osteosarcoma subtypes
Authors: Tang Haiming , Sun Nanfei , Shen Steven
Published: September 2020

Artificial intelligence (AI) has an emerging progress in diagnostic pathology. A large number of studies of applying deep learning models to histopathological images have been published in recent years. While many studies claim high accuracies, they may fall into the pitfalls of overfitting and lack of generalization due to the high variability of the histopathological images. We use the example of Osteosarcoma to illustrate the pitfalls and how the addition of model input variability can help improve model performance. We use the publicly available osteosarcoma dataset to retrain a previously published classification model for osteosarcoma. We partition the same set of images into the training and testing datasets differently than the original study: the test dataset consists of images from one patient while the training dataset consists images of all other patients. The performance of the model on the test set using the new partition schema declines dramatically, indicating a lack of model generalization and overfitting. We also show the influence of training data variability on model performance by collecting a minimal dataset of 10 osteosarcoma subtypes as well as benign tissues and benign bone tumors of differentiation. We show the additions of more and more subtypes into the training data step by step under the same model schema yield a series of coherent models with increasing performances. In conclusion, we bring forward data preprocessing and collection tactics for histopathological images of high variability to avoid the pitfalls of overfitting and build deep learning models of higher generalization abilities.
Surface texture limits transfer ofS. aureus, T4 Bacteriophage, Influenza B virus and Human coronavirus
Authors: Liu Qi , Brookbank Lindsey , Ho Angela , Coffey Jenna , Brennan Anthony B. , Jones Christopher J.
Published: September 2020

Spread of pathogens on contaminated surfaces plays a key role in disease transmission. Surface technologies that control pathogen transfer can help control fomite transmission and are of great interest to public health. Here, we report a novel bead transfer method for evaluating fomite transmission in common laboratory settings. We show that this method meets several important criteria for quantitative test methods, including reasonableness, relevancy, resemblance, responsiveness, and repeatability, and therefore may be adaptable for standardization. In addition, this method can be applied to a wide variety of pathogens including bacteria, phage, and human viruses. Using the bead transfer method, we demonstrate that an engineered micropattern limits transfer ofStaphylococcus aureusby 97.8% and T4 bacteriophage by 93.0% on silicone surfaces. Furthermore, the micropattern significantly reduces transfer of influenza B virus and human coronavirus on silicone and polypropylene surfaces. Our results highlight the potential of using surface texture as a valuable new strategy in combating infectious diseases.

Importance

Disease transmission often occurs through contact with contaminated surfaces, called fomites. Efforts to reduce this method of fomite transmission include surface cleaning, personal hygiene, alteration of habits, and novel technologies to reduce pathogen spread. This manuscript presents a novel method for the consistent contamination of surfaces to mimic the transmission of pathogens via fomites. Using this method, we present a surface texture modeled on shark skin that significantly reduces the transfer of a variety of pathogens, includingStaphylococcus aureus, influenza B virus, and human coronavirus 229E. Utilization of novel technologies to limit pathogen spread can enhance existing methods of disease mitigation.
Novel artificial intelligence-driven software significantly shortens the time required for annotation in computer vision projects
Authors: Hansen Ulrik Stig , Landau Eric , Patel Mehul , Hayee Bu’Hussain
Published: September 2020

The contribution of artificial intelligence (AI) to endoscopy is rapidly expanding. Accurate labelling of source data (video frames) remains the rate-limiting step for such projects and is a painstaking, cost-inefficient, time-consuming process.

A novel software platform, Cord Vision (CdV) allows automated annotation based on ‘embedded intelligence’. The user manually labels a representative proportion of frames in a section of video (typically 5%), to create ‘micro-models’ which allow accurate propagation of the label throughout the remaining video frames. This could drastically reduce the time required for annotation. We conducted a comparative study with an open-source labelling platform (CVAT) to determine speed and accuracy of labelling.

Across 5 users, CdV resulted in a significant increase in labelling performance (p< 0.0005) compared to CVAT with micro-models achieving > 97% accuracy for bounding box placement. This advance represents a valuable first step in Al-image analysis projects.
Death associated with coronavirus (COVID-19) infection in individuals with severe mental disorders in Sweden during the early months of the outbreak – a exploratory cross-sectional analysis of a population-based register study
Authors: Maripuu Martin , Bendix Marie , Öhlund Louise , Widerström Micael , Werneke Ursula
Published: September 2020

Background

Individuals with severe mental disorder (SMD) have a higher risk of somatic comorbidity and mortality than the rest of the population. We set up a population-based study to assess whether individuals with SMD had a higher risk of death associated with a COVID-19 infection (COVID-19 associated death) than individuals without SMD.

Methods

Exploratory analysis with a cross-sectional design in the framework of a population-based register study covering the entire Swedish population. The Swedish Board for Health and Welfare (Socialstyrelsen) provided anonymised tabulated summary data for further analysis. We compared numbers of COVID-19 associated death in individuals with SMD (cases) and without SMD (controls). We calculated the odds ratio (OR) for the whole sample and by age group and four potential risk factors, namely diabetes, cardiovascular disease, hypertension, chronic lung disease.

Results

The sample comprised of 7,923,859 individuals, 103,999 with SMD and 7,819,860 controls. There were 130 (0.1%) COVID-19 associated deaths in the SMD group and 4945 (0.06%) in the control group, corresponding to an OR of 1.98 (CI 1.66-2.35; p < 0.001). The odds were fourfold in the age group between 60 and 79 years. Cardiovascular diseases increased the odds by 50%. Individuals with SMD without any of the risk factors under study had three-folds odds of COVID-19 associated death.

Conclusion

Our preliminary results suggest that individuals with SMD are a further group at increased risk of COVID-19 associated death. The factors contributing to this increased mortality risk require clarification.
GUÍA: a digital platform to facilitate result disclosure in genetic counseling
Authors: Suckiel Sabrina A. , Odgis Jaqueline A. , Gallagher Katie M. , Rodriguez Jessica E. , Watnick Dana , Bertier Gabrielle , Sebastin Monisha , Yelton Nicole , Maria Estefany , Lopez Jessenia , Ramos Michelle , Kelly Nicole , Teitelman Nehama , Beren Faygel , Kaszemacher Tom , Davis Kojo , Laguerre Irma , Richardson Lynne D. , Diaz George A. , Pearson Nathaniel M. , Ellis Stephen B. , Stolte Christian , Robinson Mimsie , Kovatch Patricia , Horowitz Carol R. , Gelb Bruce D. , Greally John M. , Bauman Laurie J. , Zinberg Randi E. , Abul-Husn Noura , Wasserstein Melissa P. , Kenny Eimear E.
Published: September 2020

Purpose

Use of genomic sequencing is increasing at a pace that requires technological solutions to effectively meet the needs of a growing patient population. We developed GUÍA, a web-based application, to enhance the delivery of genomic results and related clinical information to patients and families.

Methods

GUÍA development occurred in 5 phases: formative research, content development, user interface design, stakeholder/community member input, and web application development. Development was informed by qualitative research involving parents (N=22) whose children underwent genomic testing. Participants enrolled in the NYCKidSeq pilot study (N=18) completed structured feedback interviews post-result disclosure using GUÍA. Genetic specialists, researchers, patients, and community stakeholders provided their perspectives on GUÍA’s design to ensure technical, cultural, and literacy appropriateness.

Results

NYCKidSeq participants responded positively to the use of GUÍA to deliver their children’s results. All participants (N=10) with previous experience with genetic testing felt GUÍA improved result disclosure, and 17 (94%) participants said the content was clear.

Conclusions

GUÍA communicates complex genomic information in an understandable and personalized manner. Initial piloting demonstrated GUÍA’s utility for families enrolled NYCKidSeq pilot study. Findings from the NYCKidSeq clinical trial will provide insight into GUÍA’s effectiveness in communicating results among diverse, multilingual populations.
Pre-existing T cell memory as a risk factor for severe COVID-19 in the elderly
Authors: Bacher Petra , Rosati Elisa , Esser Daniela , Martini Gabriela Rios , Saggau Carina , Schiminsky Esther , Dargvainiene Justina , Schöder Ina , Wieters Imke , Khodamoradi Yascha , Eberhardt Fabian , Neb Holger , Sonntagbauer Michael , Vehreschild Maria J.G.T. , Conrad Claudio , Tran Florian , Rosenstiel Philip , Markewitz Robert , Wandinger Klaus-Peter , Rybniker Jan , Kochanek Matthias , Leypoldt Frank , Cornely Oliver A. , Koehler Philipp , Franke Andre , Scheffold Alexander
Published: September 2020

Coronavirus disease 2019 (COVID-19) displays high clinical variability but the parameters that determine disease severity are still unclear. Pre-existing T cell memory has been hypothesized as a protective mechanism but conclusive evidence is lacking. Here we demonstrate that all unexposed individuals harbor SARS-CoV-2-specific memory T cells with marginal cross-reactivity to common cold corona and other unrelated viruses. They display low functional avidity and broad protein target specificities and their frequencies correlate with the overall size of the CD4+ memory compartment reflecting the “immunological age” of an individual. COVID-19 patients have strongly increased SARS-CoV-2-specific inflammatory T cell responses that are correlated with severity. Strikingly however, patients with severe COVID-19 displayed lower TCR functional avidity and less clonal expansion. Our data suggest that a low avidity pre-existing T cell memory negatively impacts on the T cell response quality against neoantigens such as SARS-CoV-2, which may predispose to develop inappropriate immune reactions especially in the elderly. We propose the immunological age as an independent risk factor to develop severe COVID-19.

Key points

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Pre-existing SARS-CoV-2-reactive memory T cells are present in all humans, but have low functional avidity and broad target specificities

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Pre-existing memory T cells show only marginal cross-reactivity to common cold corona viruses

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Frequencies of pre-existing memory T cells increase with the size of the CD4+ memory compartment reflecting the “immunological age” of the individual

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Low-avidity and polyclonal, but strongly enhanced SARS-CoV-2 specific T cell responses develop in severe COVID-19, suggesting their origin from pre-existing memory

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The immunological age may represent a risk factor to develop severe COVID-19
Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent
Authors: Chakravorty Samya , Nallamilli Babi Ramesh Reddy , Khadilkar Satish , Singla Madhubala , Bhutada Ashish , Dastur Rashna , Gaitonde Pradnya , Rufibach Laura , Gloster Logan , Hegde Madhuri
Published: September 2020

Objective

Inherited myopathies comprise more than 200 different individually rare disease-subtypes but when combined together have a high prevalence of 1 in 6000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent.

Methods

In this cohort-study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities.

Results

Clinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42%-56%) of patients with the major contributing pathogenicity in either of three genes,GNE(28%; GNE-myopathy),DYSF(25%; Dysferlinopathy) andCAPN3(19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. 78% of theDYSFpatients were homozygous for the detected pathogenic variant suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies(SGCA/B/D/G), Collagenopathy(COL6A1/2/3), Anoctaminopathy(ANO5), telethoninopathy(TCAP), Pompe-disease(GAA), Myoadenylate-deaminase-deficiency-myopathy(AMPD1), myotilinopathy(MYOT), laminopathy(LMNA), HSP40-proteinopathy(DNAJB6), Emery-Dreifuss-muscular-dystrophy(EMD), Filaminopathy(FLNC), TRIM32-proteinopathy(TRIM32), POMT1-proteinopathy(POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1(LAMA2). 13 Patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity / digenic-contribution to disease presentation and progression.

Conclusions

Application of clinically-correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically-driven molecular diagnostics.
Disease control as an optimization problem
Authors: Navascués Miguel , Budroni Costantino , Guryanova Yelena
Published: September 2020

Traditionally, expert epidemiologists devise policies for disease control through a mixture of intuition and brute force. Namely, they use their know-how to narrow down the set of logically conceivable policies to a small family described by a few parameters, following which they conduct a grid search to identify the optimal policy within the set. This scheme is not scalable, in the sense that, when used to optimize over policies which depend on many parameters, it will likely fail to output an optimal disease policy in time for its implementation. In this article, we use techniques from convex optimization theory and machine learning to conduct optimizations over disease policies described by hundreds of parameters. In contrast to past approaches for policy optimization based on control theory, our framework can deal with arbitrary uncertainties on the initial conditions and model parameters controlling the spread of the disease. In addition, our methods allow for optimization over weekly-constant policies, specified by either continuous or discrete government measures (e.g.: lockdown on/off). We illustrate our approach by minimizing the total time required to eradicate COVID-19 within the Susceptible-Exposed-Infected-Recovered (SEIR) model proposed by Kissler et al. (March, 2020).
National Longitudinal Mediators of Psychological Distress During Stringent COVID-19 Lockdown
Authors: Bulbulia Joseph A. , Piven Sofia D. , Barlow Fiona Kate , Davis Don E. , Greaves Lara M. , Highland Benjamin , Houkamau Carla A. , Milfont Taciano L. , Osborne Danny , Overall Nickola Christine , Shaver John H. , Troughton Geoffrey , Wilson Marc , Yogeeswaran Kumar , Sibley Chris G.
Published: September 2020

We leverage powerful time-series data from a national longitudinal sample measured before the COVID-19 pandemic and during the world’s eighth most stringent COVID-19 lockdown (New Zealand, March-April 2020,N= 940) and apply Bayesian multilevel mediation models to rigorously test five theories of pandemic distress. Findings: (1) during lockdown, rest diminished distress; without rest psychological distress would have been ~ 1.74 times greater; (2) an elevated sense of community reduced distress, a little, but elevated government satisfaction was inert. Thus, the psychological benefits of lockdown extended to political discontents; (3) most lockdown distress arose from dissatisfaction from personal relationships. Social captivity, more than isolation, proved challenging; (4-5) Health and business satisfaction were stable; were they challenged substantially more distress would have ensued. Thus, lockdown benefited psychological health by affording safety, yet only because income remained secure. These national longitudinal findings clarify the mental health effects of stringent infectious disease containment.
Drug library screen identifies inhibitors of toxic astrogliosis
Authors: Masvekar Ruturaj , Kosa Peter , Barbour Christopher , Milstein Joshua , Bielekova Bibiana
Published: September 2020

Objective

Multiple sclerosis is a chronic neuroinflammatory disorder, in which activated immune cells directly or indirectly induce demyelination and axonal degradation. Inflammatory stimuli also change the phenotype of astrocytes, making them neurotoxic. The resulting ‘toxic astrocyte’ phenotype has been observed in animal models of neuroinflammation and in multiple sclerosis lesions. Proteins secreted by toxic astrocytes are elevated in the cerebrospinal fluid of multiple sclerosis patients and reproducibly correlate with the rates of accumulation of neurological disability and brain atrophy. This suggests a pathogenic role for neurotoxic astrocytes in multiple sclerosis.

Methods

Here, we applied a commercially available library of small molecules that are either Food and Drug Administration-approved or in clinical development to an in vitro model of toxic astrogliosis to identify drugs and signaling pathways that inhibit inflammatory transformation of astrocytes to a neurotoxic phenotype.

Results

Inhibitors of three pathways related to the endoplasmic reticulum stress: 1) proteasome, 2) heat shock protein 90 and 3) mammalian target of rapamycin reproducibly decreased inflammation-induced conversion of astrocytes to toxic phenotype. Dantrolene, an anti-spasticity drug that inhibits calcium release through ryanodine receptors expressed in the endoplasmic reticulum of central nervous system cells, also exerted inhibitory effect at in vivo achievable concentrations. Finally, we established cerebrospinal fluid SERPINA3 as a relevant pharmacodynamic marker for inhibiting toxic astrocytes in clinical trials.

Interpretation

Drug library screening provides mechanistic insight into the generation of toxic astrocytes and identifies candidates for immediate proof-of-principle clinical trial(s).
Age-specific gene signatures underlying the transcriptomes and functional connectomes of human cerebral cortex
Authors: Zhao Xingzhong , Chen Jingqi , Xiao Peipei , Feng Jianfeng , Qing Ning , Zhao Xing-Ming
Published: September 2020

The human cerebral cortex undergoes profound structural and functional dynamic variations across the lifespan, whereas the underlying molecular mechanisms remain unclear. Here, with a novel method TCA (Transcriptome-connectome Correlation Analysis), which integrates the brain functional MR magnetic resonance images and region-specific transcriptomes, we identify age-specific cortex (ASC) gene signatures for adolescence, early adulthood, and late adulthood. The ASC gene signatures are significantly correlated with the cortical thickness (P-value <2.00e-3) and myelination (P-value <1.00e-3), two key brain structural features that vary in accordance with brain development. In addition to the molecular underpinning of age-related brain functions, the ASC gene signatures allow delineation of the molecular mechanisms of neuropsychiatric disorders, such as the regulation betweenARNT2and its target geneETF1involved in Schizophrenia. We further validate the ASC gene signatures with published gene sets associated with the adult cortex, and confirm the robustness of TCA on other brain image datasets.
Study of Distinctive Diagnostic Characteristics ofChrysomphalus dictyospermiand Closely Related Species ofChrysomphalusGenus (Insecta: Sternorryncha: Coccoidea)
Authors: Gura N.A. , Shipulin A.V.
Published: September 2020

The paper presents the results of microscopic study of the basic diagnostic structures of the pygidium of the Chrysomphalus dictyospermi, which allow to distinguish this species from the closely related ones of the Chrysomphalus genus.
Membrane linkage of aStreptococcus pneumoniaeWzy capsular polysaccharide occurs through an acylglycerol
Authors: Larson Thomas R. , Yother Janet
Published: September 2020

Capsular polysaccharides (capsules) protect bacteria from environmental insults and can contribute to virulence in pathogenic bacteria. Their appropriate display on the bacterial surface is critical to their functions. In Gram-positive bacteria, most capsules are synthesized by the Wzy polymerase-dependent pathway, which is also utilized in the synthesis of many capsules and O-antigens of Gram-negative bacteria. Synthesis of capsule repeat units initiates on undecaprenyl-phosphate on the inner face of the cytoplasmic membrane, with polymerization occurring on the outer face of the membrane. In Gram-positive bacteria, the capsule can be transferred to peptidoglycan, as inStreptococcus pneumoniaewhere a direct glycosidic bond to the peptidoglycanN-acetylglucosamine occurs. InS. pneumoniae, capsule can also be detected on the membrane, and this has generally been assumed to reflect polysaccharide that is linked to undecaprenyl-phosphate and in the process of synthesis. We provide evidence here, however, that final membrane linkage occurs through an acylglycerol, and essentially all of the polysaccharide is transferred from the initial undecaprenyl-phosphate acceptor to an alternate acceptor. This step allows for recycling of undecaprenyl-phosphate and represents an additional terminal step in capsule synthesis. In this regard, capsule synthesis resembles that of the wall- and lipoteichoic acids ofS. pneumoniae, wherein a common repeat unit and polymer structure are synthesized by the Wzy pathway with divergence at the terminal step that results in linkages to peptidoglycan and a membrane acylglycerol anchor.

IMPORTANCE

Linkage of capsular polysaccharides to the bacterial cell surface is a critical step in assuring the ability of these polymers to fulfill their functions, such as the resistance to complement-mediated phagocytosis that can be essential for pathogenic organisms to survive in host environments. Knowledge of the mechanisms by which these linkages occur is incomplete. In this study, we provide evidence for linkage of anS. pneumoniaeWzy capsule to an acylglycerol, the most abundant class of lipids in the membrane. This linkage provides a terminal acceptor for capsule that occurs in addition to that of peptidoglycan. Transfer to these terminal receptors is an essential step in CPS synthesis, as failure to do so can be lethal for the cell.
Are local dominance and inter-clade dynamics causally linked when one fossil clade displaces another?
Authors: Lidgard Scott , Di Martino Emanuela , Zágoršek Kamil , Liow Lee Hsiang
Published: September 2020

Disputing the supposition that ecological competition drives macroevolutionary patterns is now a familiar goal in many fossil biodiversity studies. But it is an elusive goal, hampered by patchy sampling, few assemblage-level comparative analyses, unverified ecological equivalence of clades and a dearth of appropriate statistical tools. We address these concerns with a fortified and vetted compilation of 40190 fossil species occurrences of cyclostome and cheilostome bryozoans, a canonical example of one taxonomically dominant clade being displaced by another. Dramatic increases in Cretaceous cheilostome genus diversification rates begin millions of years before cheilostomes overtake cyclostomes in local species proportions. Moreover, analyses of origination and extinction rates over 150 Myr suggest that inter-clade dynamics are causally linked to each other, but not to changing assemblage-level proportions.

One Sentence Summary

Global fossil diversification rates and local taxonomic dominance are not causally linked.
Large-scale identification of ubiquitination sites on membrane-associated proteins inArabidopsis thalianaseedlings
Authors: Grubb Lauren E. , Derbyshire Paul , Dunning Katherine , Zipfel Cyril , Menke Frank L.H. , Monaghan Jacqueline
Published: September 2020

Protein phosphorylation and ubiquitination are two of the most abundant forms of post-translational modifications in eukaryotes, regulated by thousands of protein kinases, phosphatases, E3 ubiquitin ligases, and ubiquitin proteases. Although previous studies have catalogued several ubiquitinated proteins in plants (Walton et al., 2016), few membrane-localized proteins have been identified. Receptor kinases (RKs) initiate phosphorylation signal relays that regulate plant growth, development, and stress responses. While the regulatory role of phosphorylation on protein kinase function is well-documented (Couto and Zipfel, 2016), considerably less is known about the role of ubiquitination on protein kinase function, even though protein turnover is critical to their signaling competence and cellular homeostasis. Here we describe the large-scale identification of ubiquitination sites on Arabidopsis proteins associated with or integral to the plasma membrane, including over 100 protein kinases.
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging
Authors: Wei Bowen , Wang Chenmao , Cheng Zongyue , Gan Wenbiao , Cui Meng
Published: September 2020

To understand neural circuit mechanisms underlying behavior, it is crucial to observe the dynamics of neuronal structure and function in different parts of the brain. Current imaging technologies allow cellular resolution imaging of neurons within ~1 millimeter below the cortical surface. Even for mice, the majority of brain tissue remains inaccessible. Although miniature optical imaging probes allow the access of deep brain regions, the cellular-resolution imaging is restricted to a small tissue volume. To drastically increase the tissue access volume and enable a high-throughput neurophotonic interface, we developed a clear optically matched panoramic access channel technique (COMPACT). With comparable probe dimension, COMPACT enables a two to three orders of magnitude greater tissue access volume for structural and function imaging. Leveraging the large-volume imaging capability of COMPACT, we demonstrated multiregional calcium imaging of deep brain functions associated with sleep for the first time. The compatibility of COMPACT for longitudinal large-volumein vivoimaging will be highly valuable to a variety of deep tissue imaging applications.
Myeloid cell-associated resistance to PD-1/PD-L1 blockade in urothelial cancer revealed through bulk and single-cell RNA sequencing
Authors: Wang Li , Sfakianos John P. , Beaumont Kristin G. , Akturk Guray , Horowitz Amir , Sebra Robert , Farkas Adam M. , Gnjatic Sacha , Hake Austin , Izadmehr Sudeh , Wiklund Peter , Oh William K , Szabo Peter , Wind-Rotolo Megan , Unsal-Kacmaz Kezi , Yao Xin , Schadt Eric , Sharma Padmanee , Bhardwaj Nina , Zhu Jun , Galsky Matthew D.
Published: September 2020

Adaptive immunity and tumor-promoting inflammation exist in delicate balance in individual tumor microenvironments; however, the role of this balance in defining sensitivity and resistance to PD-1/PD-L1 blockade therapy in urothelial cancer and other malignancies is poorly understood. We pursued an unbiased systems biology approach using bulk RNA sequencing data to examine pre-treatment molecular features associated with sensitivity to PD-1/PD-L1 blockade in patients with metastatic urothelial cancer and identified an adaptive_immune_response module associated with response and an inflammatory_response module and stromal module associated with resistance. We mapped these gene modules onto single-cell RNA sequencing data demonstrating the adaptive_immune_response module emanated predominantly from T, NK, and B cells, the inflammatory_response module from monocytes/macrophages, and the stromal module from fibroblasts. The adaptive_immune_response:inflammatory_response module expression ratio in individual tumors, reflecting the balance between antitumor immunity and tumor-associated inflammation and coined the 2IR score, best correlated with clinical outcomes and was validated in an independent cohort. Individual monocytes/macrophages with low 2IR scores demonstrated upregulation of proinflammatory genes including IL1B and downregulation of antigen presentation genes, were unrelated to classical M1 versus M2 polarization, and were enriched in pre-treatment peripheral blood from patients with PD-L1 blockade-resistant metastatic urothelial cancer.

Single sentence summary

Proinflammatory monocytes/macrophages, present in tumor and blood, are associated with resistance to immune checkpoint blockade in urothelial cancer.
Function of the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE is evolutionarily conserved in embryophytes
Authors: Kriegshauser Lucie , Knosp Samuel , Grienenberger Etienne , Tatsumi Kanade , Gütle Desirée D. , Sørensen Iben , Herrgott Laurence , Zumsteg Julie , Rose Jocelyn K.C. , Reski Ralf , Werck-Reichhart Danièle , Renault Hugues
Published: September 2020

The plant phenylpropanoid pathway generates a major class of specialized metabolites and precursors of essential extracellular polymers that initially appeared upon plant terrestrialization. Despite its evolutionary significance, little is known about the complexity and function of this major metabolic pathway in extant bryophytes, which represent the non-vascular stage of embryophyte evolution. Here, we report that theHYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE(HCT) gene that plays a critical function in the phenylpropanoid pathway during seed plant development, is functionally conserved inPhyscomitrium patens(Physcomitrella), in the moss lineage of bryophytes. Phylogenetic analysis indicates thatbonafideHCT function emerged in the progenitor of embryophytes.In vitroenzyme assays, moss phenolic pathway reconstitution in yeast andin plantagene inactivation coupled to targeted metabolic profiling, collectively indicate thatP. patensHCT (PpHCT), similar to tracheophyte HCT orthologs, uses shikimate as a native acyl acceptor to produce ap-coumaroyl-5-O-shikimate intermediate. Phenotypic and metabolic analyses of loss-of-function mutants show that PpHCT is necessary for the production of caffeate derivatives, including previously reported caffeoyl-threonate esters, and for the formation of an intact cuticle. Deep conservation of HCT function in embryophytes is further suggested by the ability ofHCTgenes fromP. patensand the liverwortMarchantia polymorphato complement anArabidopsis thalianaCRISPR/Cas9hctmutant, and by the presence of phenolic esters of shikimate in representative species of the three bryophyte lineages.
IL-6 Trans-Signaling and Crosstalk Among Tumor, Muscle and Fat Mediate Pancreatic Cancer Cachexia
Authors: Rupert Joseph E. , Bonetto Andrea , Narasimhan Ashok , Liu Yunlong , O’Connell Thomas M. , Koniaris Leonidas G. , Zimmers Teresa A.
Published: September 2020

Most patients with pancreatic adenocarcinoma (PDAC) suffer unintentional weight loss, or cachexia. Interleukin-6 causes cachexia in mice and associates with mortality in PDAC. Here we show that tumor cell-derived IL-6 mediates crosstalk between tumor and peripheral tissues to promote cachexia. Tumor-cell IL-6 elicits expression of IL-6 in fat and IL-6 and IL-6 receptor (IL6R) in muscle, concomitantly raising both in blood. Inflammation-induced adipose lipolysis elevates circulating fatty acids, which cooperate with IL-6 to induce skeletal muscle dysmetabolism and wasting. Thus, PDAC induces crosstalk among tumor, fat and muscle via a feed-forward, IL-6 signaling loop. Tumor talks to muscle and fat through IL-6, and muscle to fat via IL6R trans-signaling, and fat to muscle through lipids and fatty acids. Disruption of this crosstalk by depletion of tumor-derived IL-6 halved fat wasting and abolished muscle loss, supporting IL-6, IL-6R and lipids as causal nodes for tissue crosstalk in PDAC cachexia.

Significance

PDAC-associated cachexia significantly increases patient morbidity and mortality. This study identifies muscle and fat crosstalk via IL6R trans-signaling in concert with muscle steatosis as a main driver of PDAC-associated cachexia.
Novel genetic variants associated with brain functional networks in 18,445 adults from the UK Biobank
Authors: Foo Heidi , Thalamuthu Anbupalam , Jiang Jiyang , Koch Forrest C. , Mather Karen A. , Wen Wei , Sachdev Perminder S.
Published: September 2020

This is the first study investigating the genetics of weighted functional brain network graph theory measures from 18,445 participants of the UK Biobank (44-80 years). The eighteen measures studied showed low heritability (mean h2SNP=0.12) and were highly genetically correlated. Genome-wide association studies for these measures observed 14 significant variants associated with strength of somatomotor and limbic networks. These intergenic variants were located near thePAX8gene on chromosome 2. Gene-based analyses identified five significantly associated genes for five of the network measures, which have been implicated in sleep duration, neuronal differentiation/development, cancer, and susceptibility to neurodegenerative diseases. Genetic correlations with other traits were examined and significant correlations were observed with sleep measures and psychiatric symptoms. Further analysis found that somatomotor network strength was phenotypically associated with sleep duration and insomnia. Single nucleotide polymorphism (SNP) and gene level associations with functional network measures were identified, which may help uncover novel biological pathways relevant to human brain functional network integrity and diseases that affect it.
The Impact of The Hydroxymethyl-Cytosine Epigenetic Signature on DNA Structure And Function
Authors: Battistini Federica , Dans Pablo D. , Terrazas Montserrat , Castellazzi Chiara L. , Portella Guillem , Labrador Mireia , Villegas Núria , Brun-Heath Isabelle , González Carlos , Orozco Modesto
Published: September 2020

We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties not too different to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methyl-cytosine (mC) and 5-hydroxymethyl-cytosine (hmC) generally lead to more rigid duplexes with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). On the contrary, our simulations suggest that methylated-DNA binding domains (MBD), associated with repression activities, are very sensitive to the substitution d(mCpG)→ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) → d(hmCpG) change. Overall, while changes in gene activity due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.
Alterations to the cardiac metabolome induced by chronicT. cruziinfection relate to the degree of cardiac pathology
Authors: Hoffman Kristyn , Liu Zongyuan , Hossain Ekram , Bottazzi Maria Elena , Hotez Peter J. , Jones Kathryn M. , McCall Laura-Isobel
Published: September 2020

Chronic Chagasic cardiomyopathy (CCC) is a Neglected Tropical Disease caused by the parasiteTrypanosoma cruzi. The pathognomonic findings in symptomatic CCC patients and animal models includes diffuse cardiac fibrosis and inflammation with persistent parasite presence in the heart. This study investigated chemical alterations in different regions of the heart in relation to cardiac pathology indicators to better understand the long-term pathogenesis of this neglected disease. We used data from echocardiography, fibrosis biomarkers, and histopathological analysis to fully evaluate cardiac pathology. Metabolites isolated from the pericardial and endocardial sides of the right ventricular myocardium were analyzed by liquid chromatography tandem mass spectrometry. The endocardial sections contained significantly less cardiac inflammation and fibrosis than the pericardial sections. Cardiac levels of acylcarnitines, phosphocholines, and other metabolites were significantly disrupted in accordance with cardiac fibrosis, inflammation, and serum fibrosis biomarker levels. These findings have potential implications in treatment and monitoring for CCC patients.
Monocytes and macrophages, targets of SARS-CoV-2: the clue for Covid-19 immunoparalysis
Authors: Boumaza Asma , Gay Laetitia , Mezouar Soraya , Diallo Aïssatou Bailo , Michel Moise , Desnues Benoit , Raoult Didier , Scola Bernard La , Halfon Philippe , Vitte Joana , Olive Daniel , Mege Jean-Louis
Published: September 2020

To date, the Covid-19 pandemic affected more than 18 million individuals and caused more than 690, 000 deaths. Its clinical expression is pleiomorphic and severity is related to age and comorbidities such as diabetes and hypertension. The pathophysiology of the disease relies on aberrant activation of immune system and lymphopenia that has been recognized as a prognosis marker. We wondered if the myeloid compartment was affected in Covid-19 and if monocytes and macrophages could be infected by SARS-CoV-2. We show here that SARS-CoV-2 efficiently infects monocytes and macrophages without any cytopathic effect. Infection was associated with the secretion of immunoregulatory cytokines (IL-6, IL-10, TGF-β) and the induction of a macrophagic specific transcriptional program characterized by the upregulation of M2-type molecules. In addition, we found thatin vitromacrophage polarization did not account for the permissivity to SARS-CoV-2, since M1-and M2-type macrophages were similarly infected. Finally, in a cohort of 76 Covid-19 patients ranging from mild to severe clinical expression, all circulating monocyte subsets were decreased, likely related to massive emigration into tissues. Monocytes from Covid-19 patients exhibited decreased expression of HLA-DR and increased expression of CD163, irrespective of the clinical status. Hence, SARS-CoV-2 drives circulating monocytes and macrophages inducing immunoparalysis of the host for the benefit of Covid-19 disease progression.
Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19
Authors: Salguero Francisco J. , White Andrew D. , Slack Gillian S. , Fotheringham Susan A. , Bewley Kevin R. , Gooch Karen E. , Longet Stephanie , Humphries Holly E. , Watson Robert J. , Hunter Laura , Ryan Kathryn A. , Hall Yper , Sibley Laura , Sarfas Charlotte , Allen Lauren , Aram Marilyn , Brunt Emily , Brown Phillip , Buttigieg Karen R. , Cavell Breeze E. , Cobb Rebecca , Coombes Naomi S. , Daykin-Pont Owen , Elmore Michael J. , Gkolfinos Konstantinos , Godwin Kerry J. , Gouriet Jade , Halkerston Rachel , Harris Debbie J. , Hender Thomas , Ho Catherine M.K. , Kennard Chelsea L. , Knott Daniel , Leung Stephanie , Lucas Vanessa , Mabbutt Adam , Morrison Alexandra L. , Ngabo Didier , Paterson Jemma , Penn Elizabeth J. , Pullan Steve , Taylor Irene , Tipton Tom , Thomas Stephen , Tree Julia A. , Turner Carrie , Wand Nadina , Wiblin Nathan R. , Charlton Sue , Hallis Bassam , Pearson Geoffrey , Rayner Emma L. , Nicholson Andrew G. , Funnell Simon G. , Dennis Mike J. , Gleeson Fergus V. , Sharpe Sally , Carroll Miles W.
Published: September 2020

A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. Immune responses against SARS-CoV-2 were also similar in both species and equivalent to those reported in milder infections and convalescent human patients. Importantly, we have devised a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks.
Topoisomerase II deficiency leads to a postreplicative structural shift in all Saccharomyces cerevisiae chromosomes
Authors: Ayra-Plasencia Jessel , Ramos-Pérez Cristina , Santana-Sosa Silvia , Quevedo Oliver , Medina-Suarez Sara , Matos-Perdomo Emiliano , Zamora-Dorta Marcos , Brown Grant W , Lisby Michael , Machín Félix
Published: September 2020

The key role of Topoisomerase II (Top2) is the removal of topological intertwines between sister chromatids. In yeast, inactivation of Top2 brings about distinct cell cycle responses. In the case of the conditional top2-5 allele, interphase and mitosis progress on schedule but cells suffer from a segregation catastrophe. We here show that top2-5 chromosomes fail to enter a Pulsed-Field Gel Electrophoresis (PFGE) in the first cell cycle, a behavior traditionally linked to the presence of replication and recombination intermediates. We distinguished two classes of affected chromosomes: the rDNA-bearing chromosome XII, which fails to enter a PFGE at the beginning of S-phase, and all the other chromosomes, which fail at a postreplicative stage. In synchronously cycling cells, this late PFGE retention is observed in anaphase; however, we demonstrate that this behavior is independent of cytokinesis, stabilization of anaphase bridges, spindle pulling forces and even anaphase onset. Strikingly, once the PFGE retention has occurred it becomes refractory to Top2 re-activation. DNA combing, two-dimensional electrophoresis, genetic analyses and GFP-tagged DNA damage markers suggest that non-recombinational modifications of late replication intermediates may account for the shift in the PFGE behavior. The fact that this shift does not trigger G2/M checkpoints further supports this statement since checkpoints are active for other replicative stresses in the absence of Top2. We propose that the prolonged absence of Top2 activity leads to a general chromosome structural change. This change might interlock chromatids together with catenations and thus contribute to the formation of anaphase bridges in top2 mutants.
Existence of log-phase Escherichia coli persisters and lasting memory of a starvation pulse
Authors: Svenningsen Mikkel Skjoldan , Svenningsen Sine Lo , Sørensen Michael Askvad , Mitarai Namiko
Published: September 2020

The vast majority of a bacterial population is quickly killed when treated with a lethal concentration of antibiotics. The time scale of this killing is often comparable with the bacterial generation time before addition of antibiotics. Yet, a small subpopulation typically survives for an extended period. However, the long-term killing dynamics of bacterial cells has not been fully quantified even in well-controlled laboratory conditions. We constructed a week-long killing assay and followed the survival fraction ofEscherichia coliK12 exposed to a high concentration of ciprofloxacin. We found that long-term survivors were formed during exponential growth, with some cells surviving at least 7 days. The long-term dynamics contained at least three timescales, which greatly enhances predictions of the population survival time compared to the biphasic extrapolation from the short term behavior. Furthermore, we observed a surprisingly long memory effect of a brief carbon starvation pulse, which was dependent on the (p)ppGpp synthaserelA. Specifically, one hour of carbon starvation prior to antibiotics exposure increased the surviving fraction by nearly 100-fold even after 4 days of ciprofloxacin treatment.
Mutational signatures in countries affected by SARS-CoV-2: Implications in host-pathogen interactome
Authors: Singh J. , Singh H. , Hasnain S E. , Rahman S.A.
Published: September 2020

We are in the midst of the third severe coronavirus outbreak caused by SARS-CoV-2 with unprecedented health and socio-economic consequences due to the COVID-19. Globally, the major thrust of scientific efforts has shifted to the design of potent vaccine and anti-viral candidates. Earlier genome analyses have shown global dominance of some mutations purportedly indicative of similar infectivity and transmissibility of SARS-CoV-2 worldwide. Using high-quality large dataset of 25k whole-genome sequences, we show emergence of new cluster of mutations as result of geographic evolution of SARS-CoV-2 in local population (≥10%) of different nations. Using statistical analysis, we observe that these mutations have either significantly co-occurred in globally dominant strains or have shown mutual exclusivity in other cases. These mutations potentially modulate structural stability of proteins, some of which forms part of SARS-CoV-2-human interactome. The high confidence druggable host proteins are also up-regulated during SARS-CoV-2 infection. Mutations occurring in potential hot-spot regions within likely T-cell and B-cell epitopes or in proteins as part of host-viral interactome, could hamper vaccine or drug efficacy in local population. Overall, our study provides comprehensive view of emerging geo-clonal mutations which would aid researchers to understand and develop effective countermeasures in the current crisis.

Significance

Our comparative analysis of globally dominant mutations and region-specific mutations in 25k SARS-CoV-2 genomes elucidates its geo-clonal evolution. We observe locally dominant mutations (co-occurring or mutually exclusive) in nations with contrasting COVID-19 mortalities per million of population) besides globally dominant ones namely, P314L (ORF1b) and D164G (S) type. We also see exclusive dominant mutations such as in Brazil (I33T in ORF6 and I292T in N protein), England (G251V in ORF3a), India (T2016K and L3606F in ORF1a) and in Spain (L84S in ORF8). The emergence of these local mutations in ORFs within SARS-CoV-2 genome could have interventional implications and also points towards their potential in modulating infectivity of SARS-CoV-2 in regional population.