bluuebunny/crossref_metadata_2025 huggingface dataset:
State-space optimal feedback control of optogenetically driven neural activity
Authors: Bolus M F , Willats A A , Rozell C J , Stanley G B
Published: June 2020

Objective

The rapid acceleration of tools for recording neuronal populations and targeted optogenetic manipulation has enabled real-time, feedback control of neuronal circuits in the brain. Continuously-graded control of measured neuronal activity poses a wide range of technical challenges, which we address through a combination of optogenetic stimulation and a state-space optimal control framework implemented in the thalamocortical circuit of the awake mouse.

Approach

Closed-loop optogenetic control of neurons was performed in real-time via stimulation of channelrhodopsin-2 expressed in the somatosensory thalamus of the head-fixed mouse. A state-space linear dynamical system model structure was used to approximate the light-to-spiking input-output relationship in both single-neuron as well as multi-neuron scenarios when recording from multielectrode arrays. These models were utilized to design state feedback controller gains by way of linear quadratic optimal control and were also used online for estimation of state feedback, where a parameter-adaptive Kalman filter provided robustness to model-mismatch

Main results

This model-based control scheme proved effective for feedback control of single-neuron firing rate in the thalamus of awake animals. Notably, the graded optical actuation utilized here did not synchronize simultaneously recorded neurons, but heterogeneity across the neuronal population resulted in a varied response to stimulation. Simulated multi-output feedback control provided better control of a heterogeneous population and demonstrated how the approach generalizes beyond single-neuron applications

Significance

To our knowledge, this work represents the first experimental application of state space model-based feedback control for optogenetic stimulation. In combination with linear quadratic optimal control, the approaches here should generalize to future problems involving the control of highly complex neural circuits. More generally, feedback control of neuronal circuits opens the door to adaptively interacting with the dynamics underlying sensory, motor, and cognitive signaling, enabling a deeper understanding of circuit function and ultimately the control of function in injury or disease.
SYSTEMATIC REVIEW ON EPIDEMIOLOGY, INTERVENTIONS AND MANAGEMENT OF NONCOMMUNICABLE DISEASES IN ACUTE AND EMERGENCY CARE SETTINGS IN KENYA
Authors: Ngaruiya, MD, MSc, DTM&H Christine , Kawira, MBChB Annrita , Mali, MBChB Florence , Kambua, BPharm Faith , Mwangi, MBChB Beatrice , Wambua, MBChB Mbatha , Hersey, MLS Denise , Obare, MBChB Laventa , Leff Rebecca , Wachira, MBChB Benjamin
Published: June 2020

Introduction: Mortality and morbidity from Non-Communicable Diseases (NCDs) in Africa are expected to worsen if the status quo is maintained. Emergency care settings act as a primary point of entry into the health system for a spectrum of NCD-related illnesses, however, there is a dearth of literature on this population. We conducted a systematic review assessing available evidence on epidemiology, interventions and management of NCDs in acute and emergency care settings in Kenya, the largest economy in East Africa and a medical hub for the continent. Methods: All searches were run on July 15, 2015 capturing concepts of NCDs, and acute and emergency care. The study is registered at PROSPERO (CRD42018088621). Results: We retrieved a total of 461 references, and an additional 23 articles in grey literature. 391 studies were excluded by title or abstract, and 93 articles read in full. We included 10 articles in final thematic analysis. The majority of studies were conducted in tertiary referral or private/mission hospitals. Cancer, diabetes, cardiovascular disease and renal disease were addressed. Majority of the studies were retrospective, cross-sectional in design; no interventions or clinical trials were identified. There was a lack of access to basic diagnostic tools, and management of NCDs and their complications was limited. Conclusion: There is a paucity of literature on NCDs in Kenyan emergency care settings, with particular gaps on interventions and management. Opportunities include nationally representative, longitudinal research such as surveillance and registries, as well as clinical trials and implementation science to advance evidence-based, context-specific care.
Diagnostic technology for COVID-19: comparative evaluation of antigen and serology-based SARS-CoV-2 immunoassays, and contact tracing solutions for potential use as at-home products
Authors: Jorfi Mehdi , Luo Nell Meosky , Hazra Aditi , Herisson Fanny , Miller Glenn , Toombs James A. , Walt David R. , Bonato Paolo , Ahmad Rushdy ,   COVID-19 Direct-to-Consumer Task Force Investigators
Published: June 2020

As the United States prepares to return to work and open up the economy in the midst of the COVID-19 pandemic without an available vaccine or effective therapy, testing and contact tracing are essential to contain and limit the spread of the COVID-19 virus. In response to the urgent public health need for accurate, effective, low-cost, and scalable COVID-19 testing technology, we evaluated and identified diagnostic solutions with potential for use as an at-home product. We conducted a deep horizon scan for antigen and serology-based diagnostics and down-selected to the most promising technologies. A total of 303 candidate products (138 antibody and 44 antigen tests) were identified. Product evaluations were based entirely on company-provided data. 73 serology-based antibody tests passing an initial scoring algorithm based on specificity and sensitivity data were then further evaluated using a second scoring algorithm. This second algorithm included a review of additional technical specifications of the devices, an analysis of supply chain, manufacturing, and distribution capacity of each vendor. 24 potential antibody products met the selection criteria for further direct laboratory evaluation. The performance metrics for selection of these 24 products are currently being evaluated in a Mass General Brigham laboratory. Testing alone might not be sufficient to prevent the spread of a highly contagious disease like COVID-19. Manual contact tracing could complement testing, but it is likely to fail in identifying many individuals who were in contact with a given COVID patient. The proliferation of smartphones in the population has enabled the development of solutions that can provide public health officials with valuable information for rapid and accurate contact tracing. Besides, electronic-based contact tracing solutions can be augmented by symptom self-reports gathered using electronic patient reported outcome (ePRO) platforms and by physiological data collected using wearable sensors. We performed a detailed assessment of 12 ePRO solutions, 27 wearable sensors, and 44 electronic-based contact tracing solutions. These technologies were evaluated using criteria developed to assess their suitability to address the COVID-19 pandemic. We identified a number of solutions that could augment if not provide a more effective alternative to manual contact tracing. Finally, we propose a theoretical framework in which ePRO platforms, wearable sensors, and electronic-based contact tracing solutions would be utilized in combination with molecular and serological tests to identify and isolate COVID-19 cases rapidly.
Highly efficient intercellular spreading of protein misfolding mediated by viral ligand - receptor interactions
Authors: Liu Shu , Hossinger Andre , Hornberger Annika , Buravlova Oleksandra , Müller Stephan , Lichtenthaler Stefan F. , Neumann Manuela , Denner Philip , Vorberg Ina M.
Published: June 2020

Pathological protein aggregates associated with neurodegenerative diseases have the ability to transmit to unaffected cells, thereby templating their own aberrant conformation onto soluble proteins of the same kind. Proteopathic seeds can be released into the extracellular space, secreted in association with extracellular vesicles (EV) or exchanged by direct cell-to-cell contact. The extent to which each of these pathways contributes to the prion-like spreading of protein misfolding is unclear. Exchange of cellular cargo by both direct cell-to-cell contact as well as via EV depends on receptor-ligand interactions and subsequent release of cargo into the cytosol. We hypothesized that enabling these interactions through viral ligands enhances the aggregate-inducing capacity of EV-associated proteopathic seeds. Using different cellular models propagating model prion-like protein aggregates, mouse-adapted prions or pathogenic Tau aggregates, we demonstrate that vesicular stomatitis virus glycoprotein and SARS-CoV-2 spike S increase protein aggregate induction by direct cell-to-cell contact or via viral glycoprotein-decorated EV. Thus, receptor-ligand interactions are major determinants of intercellular aggregate dissemination. Further, our data raise the intriguing possibility that acute or latent viral infections contribute to proteopathic seed spreading by facilitating intercellular cargo transfer.

HIGHLIGHTS

Different types of proteopathic seeds are secreted in association with extracellular vesicles

Receptor-ligand interactions are important drivers of direct cell-to-cell and extracellular vesicle-mediated spreading of protein misfolding

Viral glycoproteins mediating attachment and membrane fusion strongly enhance aggregate inducing capacity in recipient cells

GRAPHICAL ABSTRACT
Abundance data applied to a novel model invertebrate host sheds new light on parasite community assembly in nature
Authors: Brian Joshua I. , Aldridge David C.
Published: June 2020

Understanding how environmental drivers influence the construction of parasite communities, in addition to how parasites may interact at an infracommunity level, are fundamental requirements for the study of parasite ecology. Knowledge of how parasite communities are assembled will help to predict the risk of parasitism for hosts, and model how parasite communities may change under variable conditions. However, studies frequently rely on presence-absence data and examine multiple host species or sites, metrics which may be too coarse to characterise nuanced within-host patterns. Here, we utilise a novel host system, the freshwater musselAnodonta anatina, to investigate how both the presence and abundance of 14 parasite taxa correlate with environmental drivers across 720 replicate parasite infracommunities. Using both redundancy analysis and a joint species distribution model, we model the impact of both host-level and environment-level characteristics on parasite structure, as well as parasite-parasite correlations after accounting for all other factors. We demonstrate that both niche- and neutral-based factors are important but to varying degrees across parasite species, suggesting that applying generalities to parasite community construction is too simplistic. Further, we show that presence-absence data fails to capture important density-dependent effects of parasite load for parasites with high abundance. Finally, we highlight that predicted parasite interaction networks vary greatly depending on whether abundance or presence-absence data is used. Our results emphasise the multi-faceted nature of parasite community assembly, and that future studies require careful consideration of the data used to infer community structure.
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images
Authors: Masci Anna Maria , White Scott , Neely Ben , Ardini-Polaske Maryanne , Hill Carol B. , Misra Ravi S , Aronow Bruce , Gaddis Nathan , Wert Susan E. , Palmer Scott M. , Chan Cliburn ,   LungMAP Consortium
Published: June 2020

Background

Immunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple cell types. For images of the developmental mouse lung, these cells are themselves organized into densely packed higher-level anatomical structures. These types of images can be challenging to segment automatically for several reasons, including the relevance of biomedical context, dependence on the specific set of probes used, prohibitive cost of generating labeled training data, as well as the complexity and dense packing of anatomical structures in the image. The use of an application ontology surmounts these challenges by combining image data with its metadata to provide a meaningful biological context, and hence constraining and simplifying the process of segmentation and object identification.

Results

We propose an innovative approach for the automated analysis of complex and densely packed anatomical structures from immunofluorescent images that utilizes an application ontology to provide a simplified context for image segmentation and object identification. We describe how the logical organization of biological facts in the form of an ontology can provide useful constraints that enhance automatic processing of complex images. We demonstrate the results of ontology-guided segmentation and object identification in mouse developmental lung images from the Bioinformatics REsource ATlas for the Healthy lung (BREATH) database of the Molecular Atlas of Lung Development (LungMAP1) program.

Conclusion

The microscopy analysis pipeline library (micap) is available athttps://github.com/duke-lungmap-team/microscopy-analysis-pipeline. Code to reproduce our analysis of LungMAP images is also available athttps://github.com/duke-lungmap-team/lungmap-pipeline. Finally, the application ontology is available athttps://github.com/duke-lungmap-team/lung_ontologyand includes example SPARQL queries.

Contact

Anna Maria Masci email:annamaria.masci@duke.edu
Baricitinib restrains the immune dysregulation in COVID-19 patients
Authors: Bronte Vincenzo , Ugel Stefano , Tinazzi Elisa , Vella Antonio , De Sanctis Francesco , Canè Stefania , Batani Veronica , Trovato Rosalinda , Fiore Alessandra , Petrova Varvara , Hofer Francesca , Barouni Roza Maria , Musiu Chiara , Caligola Simone , Pinton Laura , Torroni Lorena , Polati Enrico , Donadello Katia , Friso Simonetta , Pizzolo Francesca , Iezzi Manuela , Facciotti Federica , Pelicci Piergiuseppe , Righetti Daniela , Bazzoni Paolo , Rampudda Mariaelisa , Comel Andrea , Mosaner Walter , Lunardi Claudio , Olivieri Oliviero
Published: June 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing pandemic coronavirus disease 2019 (COVID-19). The majority of patients with COVID-19 have a good prognosis, but variable percentages in different countries develop pneumonia associated with lymphocytopenia and severe inflammatory response due to uncontrolled release of cytokines. These immune mediators are transcriptionally regulated by JAK-STAT molecular pathways, which can be disabled by small molecules. Here, we provide evidences on the efficacy of baricitinib, a JAK1/JAK2 inhibitor, in correcting the immune abnormalities observed in patients hospitalized with COVID-19. Indeed, we demonstrate a significant reduction in serum levels of interleukin (IL)-6, IL-1β and tumor necrosis factor (TNF)α, a rapid recovery in circulating T and B cell frequencies and an increased antibody production against SARS-CoV-2 spike protein in baricitinib-treated patients. Moreover, treated patients underwent a rapid reduction in oxygen flow need and progressive increase in the P/F. Our work provides the basis on developing effective treatments against COVID-19 pathogenesis using on-target therapy.
Genomic epidemiology of SARS-CoV-2 in Colombia
Authors: Laiton-Donato Katherine , Villabona-Arenas Christian Julián , Usme-Ciro José A. , Franco-Muñoz Carlos , Álvarez-Díaz Diego A. , Villabona-Arenas Liz Stephany , Echeverría-Londoño Susy , Cucunubá Zulma M. , Franco-Sierra Nicolás D. , Flórez Astrid C. , Ferro Carolina , Ajami Nadim J. , Walteros Diana Marcela , Prieto Franklin , Durán Carlos Andrés , Ospina-Martínez Martha Lucia , Mercado-Reyes Marcela
Published: June 2020

Coronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SARS-CoV-2 into the country are limited. Here, we sequenced SARS-CoV-2 from 43 clinical samples and—together with other 73 genomes sequences available from the country—we investigated the emergence and the routes of importation of COVID-19 into Colombia using epidemiological, historical air travel and phylogenetic observations. Our study provided evidence of multiple introductions, mostly from Europe, with at least 12 lineages being documented. Phylogenetic findings validated the lineage diversity, supported multiple importation events and the evolutionary relationship of epidemiologically-linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigation.
Macrophage expression and prognostic significance of the long pentraxin PTX3 in COVID-19
Authors: Brunetta Enrico , Folci Marco , Bottazzi Barbara , De Santis Maria , Protti Alessandro , Mapelli Sarah , Leone Roberto , My Ilaria , Bacci Monica , Zanon Veronica , Spata Gianmarco , Gianatti Andrea , Sironi Marina , Angelini Claudio , Garlanda Cecilia , Ciccarelli Michele , Cecconi Maurizio , Mantovani Alberto
Published: June 2020

PTX3 is an essential component of humoral innate immunity, involved in resistance to selected pathogens and in the regulation of inflammation. PTX3 plasma levels are associated with poor outcome in systemic inflammatory conditions and vascular pathology. The present study was designed to assess expression and significance of PTX3 in COVID-19. By bioinformatics analysis of public databases PTX3 expression was detected in lung respiratory cell lines exposed to SARS-CoV-2. By analysis at single cell level of COVID-19 circulating mononuclear cells, we found that PTX3 was selectively expressed by monocytes among circulating leukocytes. Moreover, in lung bronchoalveolar lavage fluid, single cell analysis revealed selective expression of PTX3 in neutrophils and macrophages, which play a major role in the pathogenesis of the disease. By immunohistochemistry, PTX3 was expressed by lung myelomocytic cells, type 2 pneumocytes and vascular endothelial cells. PTX3 plasma levels were determined by ELISA in 96 consecutive patients with a laboratory-confirmed diagnosis of COVID-19. Higher PTX3 plasma levels were observed in 52 (54.2%) patients admitted in ICU (median 21.0ng/mL, IQT 15.5-46.3 vs 12.4ng/mL IQT 6.1-20.2 in ward patients; p=0.0017) and in 22 (23%) patients died by 28 days (39.8ng/mL, IQT 20.2-75.7 vs 15.7ng/mL, IQT 8.2-21.6 in survivors; p=0.0001). After determining an optimal PTX3 cut-off for the primary outcome, the Kaplan-Meier curve showed an increased mortality in patients with PTX3>22.25ng/mL (Log-rank tests p<0.0001). In Cox regression model, PTX3>22.25ng/mL showed an adjusted Hazard Ratio (aHR) of 7.6 (95%CI2.45-23.76) in predicting mortality. Performing a multivariate logistic regression including all inflammatory markers (PTX3, ferritin, D-Dimer, IL-6, and CRP), PTX3 was the only marker significantly associated with death (aHR 1.13;95%CI1.02-1.24; p=0.021). The results reported here suggest that circulating and lung myelomonocytic cells are a major source of PTX3 and that PTX3 plasma levels can serve as a strong prognostic indicator of short-term mortality in COVID-19.
Oncogenesis and Aging by Isotopic Functionalizations of the Proteins and Nucleic Acids
Authors: Little Reginald B. , Uziel Orit
Published: June 2020

Although the dynamics of telomeres during the life expectancy of normal cells have been extensively studied, there are still some unresolved issues regarding this research field. For example, the conditions required for telomere shortening leading to malignant transformations are not fully understood. In this work, we mass analyzed DNA of normal and cancer cells for comparing telomere isotopic compositions of white blood cells and cancer cells. We have found that the 1327 Da and 1672 Da characteristic telomere mass to charges cause differential mass distributions of about 1 Da for determining isotopic variations among normal cells relative to cancer cells. These isotopic differences are consistent with a prior theory that replacing primordial, common isotopes of1H,12C,14N,16O,24Mg,31P and/or32S by nonprimordial, uncommon isotopes of2D,13C,15N,17O,25Mg and/or33S leads to altered enzymatic dynamics for modulating DNA and telomere codons towards transforming normal cells to cancer cells. The prior theory and current data are consistent also with a recently observed non-uniform methylation in DNA of cancer cells relative to more uniform methylation in DNA of normal cells. We observe further evidence of nonprimordial isotopic accelerations of acetylations, methylations, hydroxylations and aminations of nucleosides with alterations of phosphorylations of nucleotides for possibly explaining the induced mutations of DNA, RNA and proteins leading to cancer and more general alterations of DNA associated with aging. The different mass spectra of normal and cancer DNA may be reasoned by different functionalizations and isotopic enrichments as causing different motionally induced atomic and nucleotide orders by different nuclear magnetic moments (NMMs); many motionally induced oligonucleotides causing nanoscale disorder and chaos; and the many such motionally induced nanoscale chaoses of different genes causing order in macroscopic DNA for organelles organizations.
SMARCA4 Mutations in KRAS-mutant Lung Adenocarcinoma: A Multi-cohort Analysis
Authors: Liu Liang , Ahmed Tamjeed , Petty W. Jeffrey , Grant Stefan , Ruiz Jimmy , Lycan Thomas W. , Topaloglu Umit , Chou Ping-Chieh , Miller Lance D. , Hawkins Gregory A. , Alexander-Miller Martha A. , O’Neill Stacey S. , Powell Bayard L. , D’Agostino Ralph B. , Munden Reginald F. , Pasche Boris , Zhang Wei
Published: June 2020

Background

KRAS is a key oncogenic driver in lung adenocarcinoma (LUAD). Chromatin-remodeling gene SMARCA4 was co-mutated with KRAS in LUAD; however, the impact of SMARCA4 mutations on clinical outcome has not been adequately established. This study sought to shed light on the clinical significance of SMARCA4 mutations in LUAD.

Methods

The association of SMARCA4 mutations with survival outcomes was interrogated in 4 independent cohorts totaling 564 patients: KRAS-mutant patients with LUAD who received non-immunotherapy treatment from 1) The Cancer Genome Atlas (TCGA) and 2) the MSK-IMPACT Clinical Sequencing (MSK-CT) cohorts; and KRAS-mutant patients with LUAD who received immune checkpoint inhibitor-based immunotherapy treatment from 3) the MSK-IMPACT (MSK-IO) and 4) the Wake Forest Baptist Comprehensive Cancer Center (WFBCCC) immunotherapy cohorts.

Results

Of the patients receiving non-immunotherapy treatment, in the TCGA cohort (n=155), KRAS-mutant patients harboring SMARCA4 mutations (KS) showed poorer clinical outcome (P=6e-04 for disease-free survival (DFS) and .031 for overall survival (OS), respectively), compared to KRAS-TP53 co-mutant (KP) and KRAS-only mutant (K) patients; in the MSK-CT cohort (n=314), KS patients also exhibited shorter OS than KP (P=.03) or K (P=.022) patients. Of patients receiving immunotherapy, KS patients consistently exhibited the shortest progression-free survival (PFS; P=.0091) in the MSK-IO (n=77), and the shortest PFS (P=.0026) and OS (P=0.0014) in the WFBCCC (n=18) cohorts, respectively.

Conclusions

mutations of SMARCA4 represent a genetic factor that lead to adverse clinical outcome in lung adenocarcinoma treated by either non-immunotherapy or immunotherapy.
Incubation Period and Reproduction Number for novel coronavirus (COVID-19) infections in India
Authors: Patrikar SR , Kotwal A , Bhatti VK , Banerjee A , Chatterjee K , Kunte R , Tambe M
Published: June 2020

Novel coronavirus (COVID-19) rapidly spread from China to other parts of the world. Knowledge of incubation period and reproduction number is important in controlling any epidemic. The distribution of these parameters helps estimate the epidemic size and transmission potential of the disease. We estimated incubation period and reproduction number of COVID-19 for India utilizing data reported by Ministry of Health and Family Welfare (MoHFW), Government of India (GOI) and data in public domain. The mean incubation period seems to be larger at 6.93 (SD=±5.87, 95% CI: 6.11-7.75). and 95th percentile estimate for best fit normal distribution is 17.8 days. Weibull distribution, the best fit for the reproduction number estimated pre lockdown reproduction number as 2.6 (95% CI=2.34 - 2.86) and post lockdown reduced to 1.57 (95% CI=1.3 – 1.84) implying effectiveness of the epidemic response strategies. The herd immunity is estimated between 36-61% for R0 of 1.57 and 2.6 respectively.
Estimating the infection fatality risk of COVID-19 in New York City during the spring 2020 pandemic wave
Authors: Yang Wan , Kandula Sasikiran , Huynh Mary , Greene Sharon K. , Wye Gretchen Van , Li Wenhui , Chan Hiu Tai , McGibbon Emily , Yeung Alice , Olson Don , Fine Anne , Shaman Jeffrey
Published: June 2020

Background

As the COVID-19 pandemic continues to unfold, the infection fatality risk (IFR, i.e. risk of death among all infections including asymptomatic and mild infections) is crucial for gauging the burden of death due to COVID-19 in the coming months or years. Here we estimate the IFR of COVID-19 in New York City (NYC), the first epidemic center in the United States where the IFR remains unclear.

Methods

We developed a meta-population network model-inference system to estimate underlying SARS-CoV-2 infection rates in NYC during the 2020 spring pandemic wave using case, mortality, and mobility data. Based on these estimates, we further estimated the IFR for all ages overall and for 5 age groups (i.e. <25, 25-44, 45-64, 65-74, and 75+ years) separately, during March 1 – June 6, 2020 (i.e., before NYC began its phased reopening).

Findings

During March 1 – June 6, 2020, 205,639 laboratory-confirmed COVID-19 cases were diagnosed and 21,447 confirmed and probable COVID-19 deaths occurred among NYC residents. We estimated an overall IFR of 1.39% (95% Credible Interval: 1.04-1.77%) in NYC. Estimated IFR for the two oldest age groups (65-74 and 75+ years) was much higher than the younger age groups and about double estimates reported for elsewhere. In particular, weekly IFR was estimated as high as 6.7% for 65-74 year-olds and 19.1% for 75+ year-olds.

Interpretation

These results are based on more complete ascertainment of COVID-19-associated deaths in NYC and thus likely more accurately reflect the true, higher burden of death due to COVID-19 than previously reported elsewhere.
Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens
Authors: Papalexi Efthymia , Mimitou Eleni , Butler Andrew W. , Foster Samantha , Bracken Bernadette , Mauck William M. , Wessels Hans-Hermann , Yeung Bertrand Z. , Smibert Peter , Satija Rahul
Published: June 2020

The expression of inhibitory immune checkpoint molecules such asPD-L1is frequently observed in human cancers and can lead to the suppression of T cell-mediated immune responses. Here we apply ECCITE-seq, a technology which combines pooled CRISPR screens with single-cell mRNA and surface protein measurements, to explore the molecular networks that regulatePD-L1expression. We also develop a computational framework,mixscape, that substantially improves the signal-to-noise ratio in single-cell perturbation screens by identifying and removing confounding sources of variation. Applying these tools, we identify and validate regulators ofPD-L1, and leverage our multi-modal data to identify both transcriptional and post-transcriptional modes of regulation. In particular, we discover that the kelch-like proteinKEAP1and the transcriptional activatorNRF2, mediate levels ofPD-L1upregulation after IFNγ stimulation. Our results identify a novel mechanism for the regulation of immune checkpoints and present a powerful analytical framework for the analysis of multi-modal single-cell perturbation screens.
Quantitative trait locus mapping identifiesCol4a6as a novel regulator of striatal dopamine level and axonal branching in mice
Authors: Thomas Mélanie H. , Gui Yujuan , Garcia Pierre , Karout Mona , Jaeger Christian , Hodak Zdenka , Michelucci Alessandro , Kollmus Heike , Centeno Arthur , Schughart Klaus , Balling Rudi , Mittelbronn Michel , Nadeau Joseph H. , Williams Robert W. , Sauter Thomas , Sinkkonen Lasse , Buttini Manuel
Published: June 2020

The features of dopaminergic neurons (DAns) of nigrostriatal circuitry are orchestrated by a multitude of yet unknown factors, many of them genetic. Genetic variation between individuals at baseline can lead to differential susceptibility to and severity of diseases. As decline of DAns, a characteristic of Parkinson’s disease, heralds a significant decrease in dopamine level, measuring dopamine can reflect the integrity of DAns. To identify novel genetic regulators of the integrity of DAns, we used the Collaborative Cross (CC) mouse strains as model system to search for quantitative trait loci (QTLs) related to dopamine levels in the dorsal striatum. The dopamine levels in dorsal striatum varied greatly in the eight CC founder strains, and the differences were inheritable in 32 derived CC strains. QTL mapping in these CC strains identified a QTL associated with dopamine level on chromosome X containing 393 genes. RNA-seq analysis of the ventral midbrain of two of the founder strains with large striatal dopamine difference (C57BL/6J and A/J) revealed 24 differentially expressed genes within the QTL. The protein-coding gene with the highest expression difference wasCol4a6, which exhibited a 9-fold reduction in A/J compared to C57BL/6J, consistent with decreased dopamine levels in A/J. Publicly available single cell RNA-seq data from developing human midbrain suggests thatCol4a6is highly expressed in radial glia-like cells and neuronal progenitors, indicating possible involvement in neurogenesis. Interestingly, the lowered dopamine levels were accompanied by reduced striatal axonal branching of striatal DAns in A/J compared to C57BL/6J. BecauseCol4a6is known to control axogenesis in non-mammal model organisms, we hypothesize that different dopamine levels in mouse dorsal striatum are due to differences in axogenesis induced by varying COL4A6 levels during neural development.
SCARECROWgene function is required for photosynthetic development in maize
Authors: Hughes Thomas E. , Langdale Jane A.
Published: June 2020

C4photosynthesis in grasses relies on a specialized leaf anatomy. In maize, this ‘Kranz’ leaf anatomy is patterned in part by the duplicatedSCARECROW (SCR)genesZmSCR1andZmSCR1h. Here we show that in addition to patterning defects, chlorophyll content and levels of transcripts encoding Golden2-like regulators of chloroplast development are significantly lower inZmscr1;Zmscr1hmutants than in wild-type. These perturbations are not associated with changes in chloroplast number, size or ultrastructure. However, the maximum rates of carboxylation by ribulose bisphosphate carboxylase/oxygenase (RuBisCO, Vcmax) and phosphoenolpyruvate carboxylase (PEPC, Vpmax) are both reduced, leading to perturbed plant growth. The CO2compensation point and13C‰of Zmscr1;Zmscr1hplants are both normal, indicating that a canonical C4cycle is operating, albeit at reduced overall capacity. Taken together, our results reveal that the maizeSCRgenes, either directly or indirectly, play a role in photosynthetic development.

Significance statement

SCARECROW (SCR) is one of the best studied plant developmental regulators, however, its role in downstream plant physiology is less well-understood. Here, we have demonstrated that SCR is required to establish and/or maintain photosynthetic capacity in maize leaves.
The SAGE genetic toolkit enables highly efficient, iterative site-specific genome engineering in bacteria
Authors: Elmore Joshua R. , Dexter Gara N. , Francis Ryan , Riley Lauren , Huenemann Jay , Baldino Henri , Guss Adam M. , Egbert Robert
Published: June 2020

Sustainable enhancements to crop productivity and increased resilience to adverse conditions are critical for modern agriculture, and application of plant growth promoting rhizobacteria (PGPR) is a promising method to achieve these goals. However, many desirable PGPR traits are highly regulated in their native microbe, limited to certain plant rhizospheres, or insufficiently active for agricultural purposes. Synthetic biology can address these limitations, but its application is limited by availability of appropriate tools for sophisticated, high-throughput genome engineering that function in environments where selection for DNA maintenance is impractical. Here we present an orthogonal, Serine-integrase Assisted Genome Engineering (SAGE) system, which enables iterative, site-specific integration of up to 10 different DNA constructs at efficiency on par or better than replicating plasmids. SAGE does not require use of replicating plasmids to deliver recombination machinery, and employs a secondary serine-integrase to excise and recycle selection markers. Furthermore, unlike the widely utilized pBBR1 origin, DNA transformed using SAGE is stable without selection. We highlight SAGE’s utility by constructing a 287-member constitutive promoter library with a ∼40,000-fold dynamic range in P. fluorescens SBW25. We show that SAGE functions robustly in diverse α- and γ-proteobacteria, thus providing evidence that it will be broadly useful for engineering industrial or environmental bacteria.
The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development
Authors: Macrae Trisha A. , Ramalho-Santos Miguel
Published: June 2020

Pluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large gene-distal blankets in pre-implantation embryos to mark promoters of developmental genes. The factors that mediate this global redistribution of H3K27me3 are unknown. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. Using an auxin-inducible degron system, we show that the deubiquitinase Usp9x is required for mouse embryonic stem (ES) cell self-renewal. Usp9x-high ES cells have high PRC2 levels and bear a chromatin and transcriptional signature of the pre-implantation embryo, whereas Usp9x-low ES cells resemble the post-implantation, gastrulating epiblast. We show that Usp9x interacts with, deubiquitinates and stabilizes PRC2. Deletion ofUsp9xin post-implantation embryos results in the derepression of genes that normally gain H3K27me3 after gastrulation, followed by the appearance of morphological abnormalities at E9.5, pointing to a recurrent link between Usp9x and PRC2 during development. Usp9x is a marker of “stemness” and is mutated in various neurological disorders and cancers. Our results unveil a Usp9x-PRC2 regulatory axis that is critical at peri-implantation and may be redeployed in other stem cell fate transitions and disease states.
Conserved Role of the Large Conductance Calcium-Activated Potassium Channel, KCa1.1, in Sinus Node Function and Arrhythmia Risk
Authors: Pineda Santiago , Nikolova-Krstevski Vesna , Leimena Christiana , Atkinson Andrew J. , Altekoester Ann-Kristin , Cox Charles D. , Jacoby Arie , Huttner Inken G. , Ju Yue-Kun , Soka Magdalena , Ohanian Monique , Trivedi Gunjan , Kalvakuri Sreehari , Johnson Renee , Molenaar Peter , Kuchar Dennis , Allen David G. , van Helden Dirk F. , Harvey Richard P. , Hill Adam P. , Bodmer Rolf , Vogler Georg , Dobrzynski Halina , Ocorr Karen , Fatkin Diane
Published: June 2020

Background

KCNMA1encodes the α-subunit of the large-conductance Ca2+-activated K+channel, KCa1.1, and lies within a linkage interval for atrial fibrillation (AF). Insights into the cardiac functions of KCa1.1 are limited andKCNMA1has not been investigated as an AF candidate gene.

Methods and Results

KCNMA1sequencing in 118 patients with familial AF identified a novel complex variant in one kindred. To evaluate potential disease mechanisms, we first evaluated the distribution of KCa1.1 in normal hearts using immunostaining and immunogold electron microscopy. KCa1.1 was seen throughout the atria and ventricles in humans and mice, with strong expression in the sinus node. In anex vivomurine sinoatrial node preparation, addition of the KCa1.1 antagonist, paxilline, blunted the increase in beating rate induced by adrenergic receptor stimulation. Knockdown of the KCa1.1 ortholog,kcnma1b, in zebrafish embryos resulted in sinus bradycardia with dilatation and reduced contraction of the atrium and ventricle. Genetic inactivation of theDrosophilaKCa1.1 ortholog,slo, systemically or in adult stages, also slowed the heartbeat and produced cardiac arrhythmias.

Electrophysiological characterization ofslo-deficient flies revealed bursts of action potentials, reflecting increased events of fibrillatory arrhythmias. Flies with cardiac-specific overexpression of the humanKCNMA1mutant also showed increased heart period and bursts of action potentials, similar to the KCa1.1 loss-of-function models.

Conclusions

Our data point to a highly conserved role of KCa1.1 in sinus node function in humans, mice, zebrafish and fly and suggest that KCa1.1 loss of function may predispose to AF.
Membrane tethering potency of Rab-family small GTPases is defined by the C-terminal hypervariable regions
Authors: Ueda Sanae , Tamura Naoki , Mima Joji
Published: June 2020

Membrane tethering is a crucial step to determine the spatiotemporal specificity of secretory and endocytic trafficking pathways in all eukaryotic endomembrane systems. Recent biochemical studies by a chemically-defined reconstitution approach reveal that, in addition to the structurally-diverse classic tethering factors such as coiled-coil tethering proteins and multisubunit tethering complexes, Rab-family small GTPases also retain the inherent membrane tethering functions to directly and physically bridge two distinct lipid bilayers by themselves. Although Rab-mediated membrane tethering reactions are fairly efficient and specific in the physiological context, its mechanistic basis is yet to be understood. Here, to explore whether and how the intrinsic tethering potency of Rab GTPases is controlled by their C-terminal hypervariable region (HVR) domains that link the conserved small GTPase domains (G-domains) to membrane anchors at the C-terminus, we quantitatively compared tethering activities of two representative Rab isoforms in humans (Rab5a, Rab4a) and their HVR-deleted mutant forms. Strikingly, deletion of the HVR linker domains enabled both Rab5a and Rab4a isoforms to enhance their intrinsic tethering potency, exhibiting 5-to 50-fold higher initial velocities of tethering for the HVR-deleted mutants than those for the full-length, wild-type Rabs. Furthermore, we revealed that the tethering activity of full-length Rab5a was significantly reduced by the omission of anionic lipids and cholesterol from membrane lipids and, however, membrane tethering driven by HVR-deleted Rab5a mutant was completely insensitive to the headgroup composition of lipids. Reconstituted membrane tethering assays with the C-terminally-truncated mutants of Rab4a further uncovered that the N-terminal residues in the HVR linker, located adjacent to the G-domain, are critical for regulating the intrinsic tethering activity. In conclusion, our current findings establish that the non-conserved, flexible C-terminal HVR linker domains define membrane tethering potency of Rab-family small GTPases through controlling the close attachment of the globular G-domains to membrane surfaces, which confers the active tethering-competent state of the G-domains on lipid bilayers.
Extracorporeal Cytokine Hemadsorption in Severe COVID-19 Respiratory Failure
Authors: Damiani Marianna , Gandini Lucia , Landi Francesco , Fabretti Fabrizio , Gritti Giuseppe , Riva Ivano
Published: June 2020

Despite the extracorporeal cytokine hemadsorption device CytoSorb was granted FDA emergency approval for critically ill COVID19 patients, to our knowledge no published studies are currently available to support its use. This manuscript reports the experience of the use of CytoSorb during COVID19 pandemic in Bergamo, Italy. In our pilot study, eleven COVID19 patients requiring invasive mechanical ventilation for a rapidly progressive ARDS were treated with 24 to 48 hours of extracorporeal cytokine hemadsorption.

Respiratory and laboratory parameters, including a full set of inflammatory cytokines, were evaluated at different time points. A significant but transient reduction of the hyperinflammatory status was observed, along with the amelioration of the clinical and respiratory parameters.

We believe that this manuscript will provide them with important preliminary data on the use of cytokine hemadsorption devices.
Quantification of Epicardial Fat Volume as a Novel Cardiovascular Risk Marker in Asymptomatic Subjects for Early Detection of Cardiovascular Disease
Authors: Shahawy Mahfouz El , Izadi Lillee , Sabatini Antonella , Tucker Susan , Patella Jessica , Shahawy Omar El , Yturralde Frederick
Published: June 2020

Epicardial fat volume (EFV), also known as epicardial adipose tissue (EAT), sometimes acts as a protector against heart problems; however, in excess volume was found to be associated with cardiovascular structural and functional abnormalities. This study aims to establish a threshold between normal and abnormal values for EFV/EAT in asymptomatic subjects, as well as to assess whether excess EFV/EAT is associated with significant structural and functional abnormalities, including coronary artery calcium score (CACS). A total of 220 asymptomatic patients, were screened utilizing Early Cardiovascular Disease Risk Score (ECVDRS), and CT for CACS and EFV/EAT quantification. Out of the 220 subjects, 69 had a 0 CACS and were included in this analysis. These 69 were then further categorized into 3 groups: Group 1 (Normal subjects; n=20) with ECVDRS < 3, and ACC/AHA risk score < 5%; Group 2 (n= 16) with elevated EFV/EAT and no abdominal visceral obesity; Group 3 (n=33) with elevated EFV/EAT and abdominal visceral obesity. The average EFV/EAT was identified to be 69 cm3± 20 in females and 68 cm3± 15 in males among Group 1, which indicate the normal values for EFV/EAT. It was also found that elevated EFV/EAT without (Group 2) or with (Group 3) abdominal visceral adiposity was associated with significant vascular abnormalities, as compared to the normal group among these populations of asymptomatic patients with 0 CACS. Elevated EFV/EAT is a novel cardiovascular risk marker regardless of gender, which might be the culprit for major cardiovascular risk factors.
Estimation of COVID-19 dynamics in the different states of the United States using Time-Series Clustering
Authors: Rojas Fernando , Valenzuela Olga , Rojas Ignacio
Published: June 2020

Estimation of COVID-19 dynamics and its evolution is a multidisciplinary effort, which requires the unification of heterogeneous disciplines (scientific, mathematics, epidemiological, biological/bio-chemical, virologists and health disciplines to mention the most relevant) to work together in a better understanding of this pandemic. Time series analysis is of great importance to determine both the similarity in the behavior of COVID-19 in certain countries/states and the establishment of models that can analyze and predict the transmission process of this infectious disease. In this contribution, an analysis of the different states of the United States will be carried out to measure the similarity of COVID-19 time series, using dynamic time warping distance (DTW) as a distance metric. A parametric methodology is proposed to jointly analyze infected and deceased persons. This metric allows to compare time series that have a different time length, making it very appropriate for studying the United States, since the virus did not spread simultaneously in all the states/provinces. After a measure of the similarity between the time series of the states of United States was determined, a hierarchical cluster was created, which makes it possible to analyze the behavioral relationships of the pandemic between different states and to discover interesting patterns and correlations in the underlying data of COVID-19 in the United States. With the proposed methodology, nine different clusters were obtained, showing a different behavior in the eastern zone and western zone of the United States. Finally, to make a prediction of the evolution of COVID-19 in the states, Logistic, Gompertz and SIR model was computed. With these mathematical model it is possible to have a more precise knowledge of the evolution and forecast of the pandemic.
Implementing the principles of Academagogy for effective learning facilitation in corporate organizations: a case study
Authors: Murthy Shekhar , Pattanayak Biswajeet
Published: June 2020

Purpose

The purpose of this study is to adapt the principles of Academagogy (McAuliffe et al., 2009; McAuliffe and Winter, 2014) in Corporate Training. Academagogy is an amalgamation of learning theories, viz. pedagogy (teacher-centered learning); andragogy (student-centered learning); and, heutagogy (self-determined learning). 10;While the original paper by McAuliffe et al. focused on the application of Academagogical principles to higher education in a university, this case study extends Academagogy into corporate training.

Design/methodology/approach

Academagogy-based learning interventions were implemented in training programs conducted at IIC Academy. The study-sample comprised 144 trainees divided into the experiment and the control groups. Academagogical interventions were applied to the experiment group, whereas the control group followed conventional methods. Controlled quasi-experiment and statistical analyses were used as research tools in this case study.

Findings

The performance scores of the participants' at entry-level were analyzed through propensity score matching and chi-square tests. The results concluded that the experiment and the control group had no selection bias. 10; 10;The treatment effect applied to the experiment group was studied using scatter-plots and effect size analyses. 10; 10;The results indicate that the academagogical interventions markedly improved behavioral and professional skills among participants of the experiment group, which showed up in their superior performance, both during training and at work.

Research limitations/implications

This case study has two major limitations, viz. the sample population was homogenous; the batch-size was limited to 15 participants, which facilitated closer monitoring of the course.

Originality/value

Academagogical interventions were implemented in a corporate setting as opposed to earlier studies which focused on a university setting and academic environs.