bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the clinical manifestations of 16p11.2 deletion syndrome: a series of developmental case reports in children
Authors: Fetit Rana , Price David J. , Lawrie Stephen M. , Johnstone Mandy
Published: July 2020

Background

Copy number variants (CNVs) are genetic rearrangements, such as deletions and duplications, which result in a deviation from the normal number of copies of a given gene segment. CNVs are implicated in many neuropsychiatric disorders. Deletions of the human chromosomal region 16p11.2 are one of the most common genetic linkages to autism spectrum disorders (ASD). However, ASD is not the only presenting feature, and many patients with 16p11.2 deletions present with a variable clinical spectrum.

Methods

To better understand the nature and presentation of the syndrome throughout development, we present three different, unrelated clinical cases of children with 16p11.2 deletion and provide a detailed description of their clinical manifestations.

Results

Cognitive and motor impairments were characteristic of all three patients with 16p11.2 deletion, despite the differences in the extent and clinical presentation of impairment. Two patients had a clinical diagnosis of ASD and one showed several ASD traits. In addition, two patients also had severe speech and language impairments, which is in line with previous reports on 16p11.2 phenotypes. Although epilepsy and obesity have been frequently associated with 16p11.2 deletion, only one patient had a diagnosis of epilepsy and none of the three cases were obese.

Conclusion

This variation in clinical phenotype renders correct clinical interpretation and diagnosis challenging. Therefore, it is critical to elucidate the variable clinical phenotypes of rare CNVs, including 16p11.2 deletions, to help guide clinical monitoring and counselling of patients and families.
New combinations, synonymy and emendations can only be proposed based on names that were previously validly published
Authors: Oren Aharon , Garrity George M.
Published: July 2020

Recently, articles were published in this journal in which new combinations were published based on basonyms that were not validly published at the time of submission, or a name not yet validly published was proposed as a later heterotypic synonym of another name. We here wish to remind authors and editors of the relevant rules of the International Code of Nomenclature of Prokaryotes that regulate the procedure for valid publication of names and specifically, of the fact that names in online pre-publication articles in the journal’s website are not validly published.
Optimisation and comparison of orthogonal methods for separation and characterisation of extracellular vesicles to investigate how representative infant milk formula is of milk
Authors: Mukhopadhya Anindya , Santoro Jessie , Moran Barry , Useckaite Zivile , O’Driscoll Lorraine
Published: July 2020

This study aimed to separate and characterise extracellular vesicles (EV) from infant milk formula (IMF) and skim milk (SM), to determine how representative the EV content of IMF is to SM. Contaminant casein micelles, due to their abundance and overlapping size, were removed followed by either differential ultracentrifugation (DUC) or gradient ultracentrifugation (GUC). Characterisation included BCA, SDS-PAGE, nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), immunoblotting, and imaging flow cytometry (IFCM). NTA reported significantly reduced concentrations of EVs/particles in IMF versus SM; TEM showed intact SM-derived EVs to sparse and disrupted EV-like structures in IMF. Compared to IMF, noticeably stronger bands for EV biomarkers were observed by immunoblotting in SM, indicating compromised EV proteins in IMF; also supported by IFCM. Altogether, we established that EVs are substantially compromised during IMF processing. Furthermore, an optimised method combining acid pre-treatment and GUC for EV separation from milk products has been established.
Biomarkers of Memory Variability in Traumatic Brain Injury
Authors: Adamovich-Zeitlin Richard , Wanda Paul A. , Solomon Ethan , Phan Tung , Lega Bradley , Jobst Barbara C. , Gross Robert E. , Ding Kan , Diaz-Arrastia Ramon , Kahana Michael J.
Published: July 2020

Traumatic brain injury (TBI) is a leading cause of cognitive disability and is often associated with significant impairment in episodic memory. In TBI survivors, as in healthy controls, there is marked variability between individuals in memory ability. Using recordings from indwelling electrodes, we characterized and compared the oscillatory biomarkers of mnemonic variability in two cohorts of epilepsy patients: a group with a history of moderate-to-severe TBI (n= 37) and a group of non-TBI controls (n= 111) closely matched for demographics and electrode coverage. Analysis of these recordings demonstrated that increased high frequency power and decreased theta power across a broad set of brain regions mark periods of successful memory formation in both groups. As features in a logistic-regression classifier, spectral power biomarkers effectively predicted recall probability, with little difference between TBI and non-TBI controls. The two groups also displayed similar patterns of theta-frequency connectivity during successful encoding periods. These biomarkers of successful memory, highly conserved between TBI patients and controls, could serve as the basis for novel therapies that target disordered memory across diverse forms of neurological disease.
Mass cytometry analysis of the NK cell receptor-ligand repertoire reveals unique differences between dengue-infected children and adults
Authors: McKechnie Julia L. , Beltrán Davis , Ferreira Anne-Maud M. , Vergara Rosemary , Saenz Lisseth , Vergara Ofelina , Estripeaut Dora , Araúz Ana B. , Simpson Laura J. , Holmes Susan , López-Vergès Sandra , Blish Catherine A.
Published: July 2020

Dengue virus (DENV) is a significant cause of morbidity in many regions of the world, with children at the greatest risk of developing severe dengue. Natural killer (NK) cells, characterized by their ability to rapidly recognize and kill virally infected cells, are activated during acute DENV infection. However, their role in viral clearance versus pathogenesis has not been fully elucidated. Our goal was to profile the NK cell receptor-ligand repertoire to provide further insight into the function of NK cells during pediatric and adult DENV infection. We used mass cytometry (CyTOF) to phenotype isolated NK cells and peripheral blood mononuclear cells (PBMCs) from a cohort of DENV-infected children and adults. Using unsupervised clustering, we found that pediatric DENV infection leads to a decrease in total NK cell frequency with a reduction in the percentage of CD56dimCD38brightNK cells and an increase in the percentage of CD56dimperforinbrightNK cells. No such changes were observed in adults. Next, we identified markers predictive of DENV infection using a differential state test. In adults, NK cell expression of activation markers, including CD69, perforin, and Fas-L, and myeloid cell expression of activating NK cell ligands, namely Fas, were predictive of infection. In contrast, NK cell expression of the maturation marker CD57 and increased myeloid cell expression of inhibitory ligands, such as HLA class I molecules, were predictive of pediatric DENV infection. These findings suggest that acute pediatric DENV infection may result in diminished NK cell activation, which could contribute to enhanced pathogenesis and disease severity.
ERβ regulated ovarian kisspeptin plays an important role in oocyte maturation
Authors: Chakravarthi V. Praveen , Ghosh Subhra , Roby Katherine F. , Wolfe Michael W. , Rumi M. A. Karim
Published: July 2020

Kisspeptin (KISS1) signaling in the hypothalamic-pituitary (H-P) axis plays essential role in regulating gonadotropin secretion. KISS1 and KISS1 receptor (KISS1R) are also expressed in the ovary; however, the role of intraovarian KISS1 signaling remains largely unclear. Granulosa cell (GC)-specific expression of KISS1, and oocyte-specific expression of KISS1R indicate that GC-derived KISS1 may act on oocytes. Expression of KISS1 in GCs is induced by gonadotropins but it is absent in estrogen receptor β knockout (Erβnull) rats. We also observed that gonadotropin stimulation failed to induce maturation ofErβnulloocytes. Interestingly, KISS1 treatment of cumulus oocyte complexes (COCs) isolated from antral follicles promotesin vitromaturation of oocytes. Treatment of oocytes with KISS1 induced intracellular Ca2+release, and increased activation of MAP kinase ERK1/2. KISS1 treatment also induced the expression of oocyte genes that are crucial for differentiation of GCs, and maturation of oocytes. Our findings suggest that ovarian KISS1-signaling plays an important role in gonadotropin induced follicle development and oocyte maturation.
Heterogeneity in signaling pathway activity within primary and between primary and metastatic breast cancer
Authors: Inda Márcia A. , van Swinderen Paul , van Brussel Anne , Moelans Cathy B. , Verhaegh Wim , van Zon Hans , Biezen Eveline den , Bikker Jan Willem , van Diest Paul J. , van de Stolpe Anja
Published: July 2020

Background

Targeted drug treatment aims to block tumor driving signaling pathways, and is generally based on analysis of one primary tumor (PT) biopsy. Phenotypic heterogeneity within primary and between primary and metastatic lesions was investigated.

Methods

Activity of androgen and estrogen receptor, PI3K-FOXO, Hedgehog, TGFβ, and Wnt signaling pathways was measured in breast cancer samples using a novel mRNA-based assay platform. Macro-scale heterogeneity analysis was performed on multiple spatially distributed PT tissue blocks from 17 luminal A-like, 9 luminal B-like, and 9 ER-negative primary breast cancers; micro-scale heterogeneity analysis was performed on four “quadrant” samples of a single tissue block of respectively 9, 4, and 4 matched PT. Samples from 6 PT with matched lymph node (LN, n=23) and 9 PT with distant metastatic sites (DS, n=12) were analyzed. Statistical variance analysis was performed with linear mixed models. A “checkerboard” model was introduced to explain the observed heterogeneity in PT.

Results

Within PT, macro-scale heterogeneity in signaling pathway activity was similar to micro-scale heterogeneity, with a possible exception of the PI3K pathway. Variation was significantly higher on microscale for Hedgehog and TGFβ pathways. While pathway activity scores correlated significantly between different locations in the PT, positive correlations decreased between PT and LN, and even more between PT and DS metastases, including the emergence of a negative correlation for the ER pathway.

Conclusion

With a possible exception of the PI3K pathway, variation in signaling pathway activity within a single PT tissue block was generally representative for the whole PT, but not for DS or LN metastases. The higher variation in TGFβ and HH pathway activity on microscale suggested the presence of multiple small cancer cell clones. While analysis of multiple sub-samples of a single biopsy block may be sufficient to predict PT response to some targeted therapies, such as hormonal therapy, metastatic breast cancer treatment requires analysis of metastatic biopsies. The findings on phenotypic intra-tumor heterogeneity are compatible with currently emerging ideas on a Big Bang type of cancer evolution.
Rationing and triage of scarce, lifesaving therapy in the context of the COVID-19 pandemic - a cross-sectional, social media-driven, scenario-based online query of societal attitudes
Authors: Muensterer Oliver J. , Gianicolo Emilio A. , Paul Norbert W.
Published: July 2020

Background

The recent COVID-19 pandemic made us aware that medical resources are limited. When demand for essential resources surpasses availability, difficult triaging decisions are necessary. While algorithms exist, almost nothing is known on societal attitudes regarding triage criteria.

Methods

A cross-sectional survey was conducted via social media channels to query a broad sample of society. Participants were asked to make triage decisions in case-based vignettes, exploring a variety of factors. They also were asked to assess how sure they were about their decisions, and how such decisions should be reached.

Results

The survey was completed in full by 1626 participants in April 2020. Median age was 39 years (range 12-80 years), 984 (61%) were female. Patient prognosis, responsibility towards others, the absence of behavior-induced co-morbidities, and younger age were rated the most important triage criteria, while participants found that insurance status, social status, and nationality should not play a substantial role. Ethics-committees and point systems were regarded potentially helpful for triage decision-making, while decisions based on order of presentation (first-come first-serve) or on a legal basis were viewed critically. Participants were least sure about their decision when dealing with age or behavior-induced co-morbidities. Overall, women were surer about their decisions than men, participants of Christian faith were also more secure about their decision than atheists-agnostics.

Conclusions

This study uses social media to generate insight into public opinion and attitudes regarding triage criteria and modalities. These findings may be helpful for the development of future medical triage algorithms.
Unemployment insurance and food insecurity among people who lost employment in the wake of COVID-19
Authors: Raifman Julia , Bor Jacob , Venkataramani Atheendar
Published: July 2020

Forty million U.S. residents lost their jobs in the first two months of the coronavirus disease 2019 (COVID-19) pandemic. In response, the Federal Government expanded unemployment insurance benefits in both size ($600/week supplement) and scope (to include caregivers and self-employed workers). We assessed the relationship between unemployment insurance and food insecurity among people who lost their jobs during the COVID-19 pandemic in the period when the federal unemployment insurance supplement was in place. We analyzed data from the Understanding Coronavirus in America (UAC) cohort, a longitudinal survey collected by the University of Southern California Center for Economic and Social Research (CESR) every two weeks between April 1 and July 8, 2020. We limited the sample to individuals living in households earning less than $75,000 in February 2020 who lost their jobs during COVID-19. Using difference-in-differences and event study regression models, we evaluated the association between receipt of unemployment insurance and self-reported food insecurity and eating less due to financial constraints. We found that 40.5% of those living in households earning less than $75,000 and employed in February 2020 experienced unemployment during the COVID-19 pandemic. Of those who lost their jobs, 31% reported food insecurity and 33% reported eating less due to financial constraints. Food insecurity peaked in April 2020 and declined over time, but began to increase again among people receiving unemployment insurance during the final wave of the survey ahead of the federal supplement to unemployment insurance ending. Food insecurity and eating less were more common among people who were non-White, lived in lower-income households, younger, and who were sexual or gender minorities. Receipt of unemployment insurance was associated with a 4.4 percentage point (95% CI: −7.8 to −0.9 percentage points) decline in food insecurity (a 30.3% relative decline compared to the average level of food insecurity during the study period). Receipt of unemployment insurance was also associated with a 6.1 percentage point (95% CI: −9.6 to −2.7 percentage point) decline in eating less due to financial constraints (a 42% relative decline). Estimates from event study specifications revealed that reductions in food insecurity and eating less were greatest in the four-week period immediately following receipt of unemployment insurance, with no evidence of differential pre-existing trends in either outcome. We conclude that receiving unemployment insurance benefits during the period when the $600/week federal supplement was in place was associated with large reductions in food insecurity.
Clinical validation of innovative, low cost, kit-free, RNA processing protocol for RT-PCR based COVID-19 testing
Authors: Sahajpal Nikhil Shri , Mondal Ashis K , Njau Allan , Ananth Sudha , Kothandaraman Arvind , Hegde Madhuri , Chaubey Alka , Padala Sandeep , Kota Vamsi , Caspary Kevin , Tompkins Stephen M , Ross Ted , Rojani Amyn M. , Kolhe Ravindra
Published: July 2020

The current gold-standard molecular diagnosis for COVID-19 is based on a multi-step assay involving RNA-extraction and RT-PCR analysis for the detection of SARS-CoV-2. RNA-extraction step has been a major rate-limiting step in implementing high-throughput screening for COVID-19 during this pandemic. Moreover, clinical laboratories are facing several challenges that include cost, reagents, instrumentation, turn-around time, trained personnel, and supply-chain constraints to efficiently implement and sustain testing. Cognizant of these limitations, we evaluated the extraction-free methods described in the literature and have developed an innovative, simplified and easy protocol employing limited reagents to extract RNA for subsequent RT-PCR analysis. Nasopharyngeal-swab samples were subjected to the following individual conditions: 65°C for 15 minutes; 80°C for 5 minutes; 90°C for 5 minutes or 80°C for 1 minute, and processed for direct RT-PCR. These groups were also compared with a supplemental protocol adding isopropanol-ethanol-water elution steps followed by RT-PCR assay. The direct RT-PCR assay did not detect SARS-CoV-2 within the various temperature incubation only groups, whereas, the 90°C for 5 minutes-isopropanol-ethanol-water method was found to be comparable to the FDA-EUA method. Evaluation of the performance metrics for 100 clinical samples demonstrated a sensitivity of 94.2% and a specificity of 100%. The limit of detection was ascertained to be ∼40 copies/ml by absolute-quantification. The protocol presented for this assay employs limited reagents and yields results with high sensitivity. Additionally, it presents a simplified methodology that would be easier to implement in laboratories in limited resource countries in order to meet the high current COVID-19 testing needs.
Optimizing antiviral treatment for seasonal influenza in the United States: A Mathematical Modeling Analysis
Authors: Yechezkel Matan , Ndeffo Mbah Martial L , Yamin Dan
Published: July 2020

Seasonal influenza remains a major health burden in the United States. Despite recommendations of early antiviral treatment of high-risk patients, the effective treatment coverage remains very low. We developed an influenza transmission model that incorporates data on infectious viral load, social contact, and healthcare-seeking behavior, to evaluate the population-level impact of increasing antiviral treatment timeliness and coverage among high-risk patients in the US. We found that increasing the rate of early treatment among high-risk patients who received treatment more than 48 hours after symptoms onset, would substantially avert infections and influenza-induced hospitalizations. We found that treatment of the elderly has the highest impact on reducing hospitalizations, whereas treating high-risk individuals aged 5-19 years old has the highest impact on transmission. The population-level impact of increased timeliness and coverage of treatment among high-risk patients was observed regardless of seasonal influenza vaccination coverage and the severity of the influenza season.
COVID-19: Time-Dependent Effective Reproduction Number and Sub-notification Effect Estimation Modeling
Authors: de Carvalho Eduardo Atem , de Carvalho Rogerio Atem
Published: July 2020

Background

Since the beginning of the COVID-19 pandemic, researchers and health authorities have sought to identify the different parameters that govern their infection and death cycles, in order to be able to make better decisions. In particular, a series of reproduction number estimation models have been presented, with different practical results.

Objective

This article aims to present an effective and efficient model for estimating the Reproduction Number and to discuss the impacts of sub-notification on these calculations.

Methods

The concept of Moving Average Method with Initial value (MAMI) is used, as well as a model for Rt, the Reproduction Number, is derived from experimental data. The models are applied to real data and their performance is presented.

Results

Analyses on Rt and sub-notification effects for Germany, Italy, Sweden, United Kingdom, South Korea, and the State of New York are presented to show the performance of the methods here introduced.

Conclusions

We show that, with relatively simple mathematical tools, it is possible to obtain reliable values for time-dependent, incubation period-independent Reproduction Numbers (Rt). We also demonstrate that the impact of sub-notification is relatively low, after the initial phase of the epidemic cycle has passed.
New measures of agency from an adaptive sensorimotor task
Authors: Wang Shiyun , Rajananda Sivananda , Lau Hakwan , Knotts J. D.
Published: July 2020

Self-agency, the sense that one is the author or owner of one’s behaviors, is impaired in multiple psychological and neurological disorders, including functional movement disorders, Parkinson’s Disease, alien hand syndrome, schizophrenia, and dystonia. Existing assessments of self-agency, many of which focus on agency of movement, can be prohibitively time-consuming and often yield ambiguous results. Here, we introduce a short online motion tracking task that quantifies movement agency through both first-order perceptual and second-order metacognitive judgments. The task assesses the degree to which a participant can distinguish between a motion stimulus whose trajectory is influenced by the participant’s cursor movements and a motion stimulus whose trajectory is random. We demonstrate the task’s reliability in healthy participants and discuss how its efficiency, reliability, and ease of online implementation make it a promising new tool for both diagnosing and understanding disorders of agency.
The construction and deconstruction of sub-optimal preferences through range-adapting reinforcement learning
Authors: Bavard Sophie , Rustichini Aldo , Palminteri Stefano
Published: July 2020

Converging evidence suggests that economic values are rescaled as a function of the range of the available options. Critically, although locally adaptive, range adaptation has been shown to lead to suboptimal choices. This is particularly striking in reinforcement learning (RL) situations when options are extrapolated from their original context. Range adaptation can be seen as the result of an adaptive coding process aiming at increasing the signal-to-noise ratio. However, this hypothesis leads to a counter-intuitive prediction: decreasing outcome uncertainty should increase range adaptation and, consequently, extrapolation errors. Here, we tested the paradoxical relation between range adaptation and performance in a large sample of subjects performing variants of a RL task, where we manipulated task difficulty. Results confirmed that range adaptation induces systematic extrapolation errors and is stronger when decreasing outcome uncertainty. Finally, we propose a range-adapting model and show that it is able to parsimoniously capture all the observed results.
Sex-Specific Genetic Architecture Of Behavioral Traits In A Spider
Authors: Kralj-Fišer Simona , Schneider Jutta M. , Kuntner M. , Garcia-Gonzalez Francisco
Published: July 2020

Sex differences in behavioral traits are common, but we know little about the role of sexual selection in shaping these traits. Estimating sex-specific genetic effects and cross-sex genetic correlations can provide insights into sex-specific selection and on whether evolution can shape independent expression of behavioral traits across the sexes. We conducted a quantitative genetic study in a sexually-size-dimorphic spider,Larinioides sclopetarius, which exhibits sex differences in adult life-styles. We observed pedigreed spiders for aggression, activity, exploration and boldness, and used animal models to disentangle genetic and environmental influences on these behaviors. We detected higher additive genetic variances in activity and aggression in males compared to females, but no sex differences in quantitative genetic estimates for exploration and boldness. The estimated mean cross-sex genetic correlation in all traits were close to zero suggesting these traits could have flexibility for sex-independent evolution. We note however, that the 95% credible intervals of cross-sex genetic correlation are large, and thus estimates uncertain. Our results imply that individual variation in aggression and activity might stem from sex-specific selection acting on these traits. The estimates of sex-specific additive genetic variation and cross-sex genetic correlation suggests their further sex-independent evolution. Taken together, our results support the notion that sexual selection can play an important role shaping behavioral traits.
ExBoX: a simple Boolean exclusion strategy to drive expression in neurons
Authors: Ubina Teresa , Vahedi-Hunter Tyler , Agnew-Svoboda Will , Wong Wenny , Gupta Akshay , Santhakumar Vijayalakshmi , Riccomagno Martin M.
Published: July 2020

The advent of modern single-cell biology has revealed the striking molecular diversity of cell populations once thought to be more homogeneous. This newly appreciated complexity has made intersectional genetic approaches essential to understanding and probing cellular heterogeneity at the functional level. Here we build on previous knowledge to develop a simple AAV-based approach to define specific subpopulations of cells by Boolean exclusion logic (AND NOT). This Expression by Boolean Exclusion (ExBoX) system encodes for a gene of interest which is turned On by a particular recombinase (Cre or FlpO) and turned Off by another. ExBoX allows for the specific transcription of a gene of interest in cells expressing only the activating recombinase, but not in cells expressing both. We show the ability of the ExBoX system to tightly regulate expression of fluorescent reportersin vitroandin vivo, and further demonstrate the adaptability of the system by achieving expression of a variety of virally-delivered coding sequences in the mouse brain. This simple strategy will expand the molecular toolkit available for cell- and time-specific gene expression in a variety of systems.

Summary statement

Ubina et al. describe the generation of a novel AAV-based intersectional approach to define and target specific subpopulations of cells in time and space via Expression by Boolean Exclusion (ExBoX).
Global drivers of obligate mycorrhizal symbionts diversification
Authors: Perez-Lamarque Benoît , Öpik Maarja , Maliet Odile , Afonso Silva Ana C. , Selosse Marc-André , Martos Florent , Morlon Hélène
Published: July 2020

Analyzing diversification dynamics is key to understanding the past evolutionary history of clades that led to present-day biodiversity patterns. While such analyses are widespread in well-characterized groups of species, they are much more challenging in groups which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyze the diversification dynamics of this clade in the past 500 million years (Myr). We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 Myr ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.
Parallel genetics of regulatory sequencesin vivo
Authors: Froehlich Jonathan , Uyar Bora , Herzog Margareta , Theil Kathrin , Glažar Petar , Akalin Altuna , Rajewsky Nikolaus
Published: July 2020

Understanding how regulatory sequences control gene expression is fundamental to explain how phenotypes arise in health and disease. Traditional reporter assays inform about function of individual regulatory elements, typically in isolation. However, regulatory elements must ultimately be understood by perturbing them within their genomic environment and developmental- or tissue-specific contexts. This is technically challenging; therefore, few regulatory elements have been characterizedin vivo. Here, we used inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3′ UTRs of 16 genes inC. elegans. To quantify the consequences of mutations on expression, we developed a targeted RNA sequencing strategy across hundreds of mutant animals. We were also able to systematically and quantitatively assign fitness cost to mutations. Finally, we identified and characterized sequence elements that strongly regulate phenotypic traits. Our approach enables highly parallelized, functional analysis of regulatory sequencesin vivo.
Effects of Kappa Opioid Receptor Agonists on Fentanyl vs. Food Choice in Male and Female Rats: Contingent vs. Non-Contingent Administration
Authors: Townsend E. Andrew
Published: July 2020

Rationale

Strategies are needed to decrease the abuse liability of mu opioid receptor (MOR) agonists. One strategy under consideration is to combine MOR agonists with kappa opioid receptor (KOR) agonists.

Objectives

The effects of KOR-agonists (U50488, nalfurafine) on fentanyl-versus-food choice were compared under conditions where the KOR agonists were added to the self-administered fentanyl (contingent delivery) or administered as pretreatments (non-contingent delivery) in male and female rats. The effects of increasing and decreasing the magnitude of the alternative food reinforcer were also determined.

Methods

Rats were trained to respond under a concurrent schedule of fentanyl (0, 0.32-10 μg/kg/infusion) and food reinforcement. In Experiment 1, U50488 and nalfurafine were co-administered with fentanyl as fixed-proportion mixtures (contingent administration). In Experiment 2, U50488 (1-10 mg/kg) and nalfurafine (3.2-32 μg/kg) were administered as acute pretreatments (non-contingent administration). nor-BNI (32 mg/kg) was administered prior to contingent and non-contingent KOR-agonist treatment in Experiment 3. Experiment 4 evaluated the effects of increasing and decreasing the magnitude of the non-drug reinforcer.

Results

Both U50488 and nalfurafine decreased fentanyl choice when administered contingently, demonstrating that KOR agonists punish opioid choice. Non-contingent U50488 and nalfurafine administration decreased rates of fentanyl and food self-administration without altering fentanyl choice. Both contingent and non-contingent U50488 and nalfurafine effects on fentanyl choice were attenuated by nor-BNI. Fentanyl choice was sensitive to increases and decreases in the magnitude of the non-drug reinforcer.

Conclusions

These results demonstrate that the effects of KOR agonists on fentanyl reinforcement are dependent upon the contingencies under which they are administered.
Biogeochemical and omic evidence for paradoxical methane production via multiple co-occurring mechanisms in aquatic ecosystems
Authors: Perez-Coronel Elisabet , Beman J. Michael
Published: July 2020

Aquatic ecosystems are globally significant sources of the greenhouse gas methane (CH4) to the atmosphere. However, CH4is produced ‘paradoxically’ in oxygenated water via poorly understood mechanisms, fundamentally limiting our understanding of overall CH4production. Here we resolve paradoxical CH4production mechanisms through CH4measurements,δ13CH4analyses, 16S rRNA sequencing, and metagenomics/metatranscriptomics applied to freshwater incubation experiments with multiple time points and treatments (addition of a methanogenesis inhibitor, dark, high-light). We captured significant paradoxical CH4production, as well as consistent metabolism of methylphosphonate by abundant bacteria—resembling observations from marine ecosystems. Metatranscriptomics andδ13CH4analyses applied to experimental treatments identified an additional CH4production mechanism associated with (bacterio)chlorophyll metabolism and photosynthesis by Cyanobacteria, and especially by Proteobacteria. Both mechanisms occured together within metagenome-assembled genomes, and appear widespread in freshwater. Our results indicate that multiple, co-occurring, and broadly-distributed bacterial groups and metabolic pathways produce CH4in aquatic ecosystems.
Efficiency of local learning rules in threshold-linear associative networks
Authors: Schönsberg Francesca , Roudi Yasser , Treves Alessandro
Published: July 2020

We show that associative networks of threshold linear units endowed with Hebbian learning can operate closer to the Gardner optimal storage capacity than their binary counterparts and even surpass this bound. This is largely achieved through a sparsification of the retrieved patterns, which we analyze for theoretical and empirical distributions of activity. As reaching the optimal capacity via non-local learning rules like back-propagation requires slow and neurally implausible training procedures, our results indicate that one-shot self-organized Hebbian learning can be just as efficient.
Discovery of a Novel, Selective and Short-Acting Skeletal Myosin II Inhibitor
Authors: Radnai Laszlo , Surman Matthew , Hafenbreidel Madalyn , Young Erica J. , Stremel Rebecca F. , Lin Li , Pasetto Paolo , Jin Xiaomin , Geedy Mackenzie , Partridge Joni-Rae , Patel Aagam , Conlon Michael , Sellers James R. , Cameron Michael D. , Rumbaugh Gavin , Griffin Patrick R. , Kamenecka Theodore M. , Miller Courtney A.
Published: July 2020

Myosin IIs, actin-based motors that utilize the chemical energy of ATP to generate force, have potential as therapeutic targets. Their heavy chains differentiate the family into muscle (skeletal [SkMII], cardiac, smooth) and nonmuscle myosin IIs. Despite therapeutic potential for muscle disorders, no SkMII-specific inhibitor has been reported and characterized. Here we present the discovery, synthesis and characterization of “skeletostatins”, novel derivatives of the pan-myosin II inhibitor blebbistatin, with selectivity within the myosin IIs for SkMII. In addition, the skeletostatins bear improved potency, solubility and photostability, without cytotoxicity. Based on its optimalin vitroprofile, Skeletostatin 1’sin vivotolerability, efficacy and pharmacokinetics were determined. Skeletostatin 1 was well-tolerated in mice, impaired motor performance, and had an excellent muscle to plasma ratio. Skeletostatins are useful probes for basic research and a strong starting point for drug development.
Structural mechanism for amino acid-dependent Rag GTPase switching by SLC38A9
Authors: Fromm Simon A. , Lawrence Rosalie E. , Hurley James H.
Published: July 2020

The mechanistic target of rapamycin complex 1 (mTORC1) couples cell growth to nutrient, energy and growth factor availability (1–3). mTORC1 is activated at the lysosomal membrane when amino acids are replete via the Rag guanosine triphosphatases (GTPases) (4–6). Rags exist in two stable states, an inactive (RagA/BGDP:RagC/DGTP) and active (RagA/BGTP:RagC/DGDP) state, during low and high cellular amino acid levels (4, 5). The lysosomal folliculin (FLCN) complex (LFC) consists of the inactive Rag dimer, the pentameric scaffold Ragulator (7, 8), and the FLCN:FNIP (FLCN-interacting protein) GTPase activating protein (GAP) complex (9), and prevents activation of the Rag dimer during amino acid starvation (10, 11). How the LFC is released upon amino acid refeeding is a major outstanding question in amino-acid dependent Rag activation. Here we show that the cytoplasmic tail of the lysosomal solute carrier family 38 member 9 (SLC38A9), a known Rag activator (12–14), destabilizes the LFC. By breaking up the LFC, SLC38A9 triggers the GAP activity of FLCN:FNIP toward RagC. We present the cryo electron microscopy (cryo-EM) structures of Rags in complex with their lysosomal anchor complex Ragulator and the cytoplasmic tail of SLC38A9 in the pre and post GTP hydrolysis state of RagC, which explain how SLC38A9 destabilizes the LFC and so promotes Rag dimer activation.
Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model
Authors: Patel Ami , Walters Jewell , Reuschel Emma L. , Schultheis Katherine , Parzych Elizabeth , Gary Ebony N. , Maricic Igor , Purwar Mansi , Eblimit Zeena , Walker Susanne N. , Guimet Diana , Bhojnagarwala Pratik , Doan Arthur , Xu Ziyang , Elwood Dustin , Reeder Sophia M. , Pessaint Laurent , Kim Kevin Y. , Cook Anthony , Chokkalingam Neethu , Finneyfrock Brad , Tello-Ruiz Edgar , Dodson Alan , Choi Jihae , Generotti Alison , Harrison John , Tursi Nicholas J. , Andrade Viviane M. , Dia Yaya , Zaidi Faraz I. , Andersen Hanne , Lewis Mark G. , Muthumani Kar , Kim J Joseph , Kulp Daniel W. , Humeau Laurent M. , Ramos Stephanie , Smith Trevor R.F. , Weiner David B. , Broderick Kate E.
Published: July 2020

Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has had a dramatic global impact on public health, social, and economic infrastructures. Here, we assess immunogenicity and anamnestic protective efficacy in rhesus macaques of the intradermal (ID)-delivered SARS-CoV-2 spike DNA vaccine, INO-4800. INO-4800 is an ID-delivered DNA vaccine currently being evaluated in clinical trials. Vaccination with INO-4800 induced T cell responses and neutralizing antibody responses against both the D614 and G614 SARS-CoV-2 spike proteins. Several months after vaccination, animals were challenged with SARS-CoV-2 resulting in rapid recall of anti-SARS-CoV-2 spike protein T and B cell responses. These responses were associated with lower viral loads in the lung and with faster nasal clearance of virus. These studies support the immune impact of INO-4800 for inducing both humoral and cellular arms of the adaptive immune system which are likely important for providing durable protection against COVID-19 disease.
Cell-to-cell Mathematical Modeling of Arrhythmia Phenomena in the Heart
Authors: Garza Gabriel López , Nicolás Mata A. , Román Alonso G. , Godínez Fernández J. F. , Castro García M. A.
Published: July 2020

With an aperiodic, self-similar distribution of two-dimensional arrangement of atrial cells, it is possible to simulate such phenomena as Fibrillation, Fluttering, and a sequence of Fibrillation-Fluttering. The topology of a network of cells may facilitate the initiation and development of arrhythmias such as Fluttering and Fibrillation. Using a GPU parallel architecture, two basic cell topologies were considered in this simulation, an aperiodic, fractal distribution of connections among 462 cells, and a chessboard-like geometry of 60×60 and 600×600 cells. With a complex set of initial conditions, it is possible to produce tissue behavior that may be identified with arrhythmias. Finally, we found several sets of initial conditions that show how a mesh of cells may exhibit Fibrillation that evolves into Fluttering.
Infection of human lymphomononuclear cells by SARS-CoV-2
Authors: Pontelli Marjorie C , Castro Italo A , Martins Ronaldo B , Veras Flávio P , Serra Leonardo La , Nascimento Daniele C , Cardoso Ricardo S , Rosales Roberta , Lima Thais M , Souza Juliano P , Caetité Diego B , de Lima Mikhael H F , Kawahisa Juliana T , Giannini Marcela C , Bonjorno Letícia P , Lopes Maria I F , Batah Sabrina S , Siyuan Li , Assad Rodrigo L , Almeida Sergio C L , Oliveira Fabiola R , Benatti Maíra N , Pontes Lorena L F , Santana Rodrigo C , Vilar Fernando C , Martins Maria A , Cunha Thiago M , Calado Rodrigo T , Alves-Filho José C , Zamboni Dario S , Fabro Alexandre , Louzada-Junior Paulo , Oliveira Rene D R , Cunha Fernando Q , Arruda Eurico
Published: July 2020

Although SARS-CoV-2 severe infection is associated with a hyperinflammatory state, lymphopenia is an immunological hallmark, and correlates with poor prognosis in COVID-19. However, it remains unknown if circulating human lymphocytes and monocytes are susceptible to SARS-CoV-2 infection. In this study, SARS-CoV-2 infection of human peripheral blood mononuclear cells (PBMCs) was investigated bothin vitroandin vivo. We found thatin vitroinfection of whole PBMCs from healthy donors was productive of virus progeny. Results revealed that monocytes, as well as B and T lymphocytes, are susceptible to SARS-CoV-2 active infection and viral replication was indicated by detection of double-stranded RNA. Moreover, flow cytometry and immunofluorescence analysis revealed that SARS-CoV-2 was frequently detected in monocytes and B lymphocytes from COVID-19 patients, and less frequently in CD4+T lymphocytes. The rates of SARS-CoV-2-infected monocytes in PBMCs from COVID-19 patients increased over time from symptom onset. Additionally, SARS-CoV-2-positive monocytes and B and CD4+T lymphocytes were detected by immunohistochemistry in post mortem lung tissue. SARS-CoV-2 infection of blood circulating leukocytes in COVID-19 patients may have important implications for disease pathogenesis, immune dysfunction, and virus spread within the host.
Corticosteroid Use in Severely Hypoxemic COVID-19 Patients: An Observational Cohort Analysis of Dosing Patterns and Outcomes in the Early Phase of the Pandemic
Authors: Rahman Omar , Trigonis Russell A. , Craft Mitchell K. , Kruer Rachel M. , Miller Emily M. , Terry Colin L. , Persaud Sarah A. , Kapoor Rajat
Published: July 2020

INTRODUCTION

Hypoxemia in Severe Acute Respiratory Syndrome due to Novel Coronavirus of 2019 (SARS-CoV-2) is mediated by severe inflammation that may be mitigated by corticosteroids. We evaluated pattern and effects of corticosteroid use in these patients during an early surge of the pandemic.

METHODS

Observational study of 136 SARS-CoV-2 patients admitted to the Intensive care Unit between March 1 and April 27, 2020 at a tertiary care hospital in Indianapolis, USA.

Statistical comparison between cohorts and dosing pattern analysis was done. Outcome measures included number of patients requiring intubation, duration of mechanical ventilation, length of ICU stay and inpatient mortality.

RESULTS

Of 136 patients, 72 (53%) received corticosteroids. Groups demographics: Age (60.5 vs. 65; p .083), sex (47% male vs. 39% female; p .338) and comorbidities were similar. Corticosteroid group had increased severity of illness: PaO2/FiO2 (113 vs. 130; p .014) and SOFA (8 vs. 5.5; p < .001). Overall mortality (21% vs. 30%; p .234) or proportion of patients intubated (78 vs. 64%; p .078) was similar. Mortality was similar among mechanically ventilated (27% vs. 15%; p .151) however there were no deaths among patients who were not mechanically ventilated and received corticosteroids (0% vs. 57%; p <.001). Early administration (within 48 hours) showed decrease in proportion of intubation (66% vs. 87 vs. 100%; p.045), ICU days (6 vs., 16 vs. 18; p <.001), and ventilator days (3 vs. 12 & 14; p <.001). 45% received methylprednisolone.

CONCLUSION

Corticosteroids were used more frequently in SARS CoV-2 patients with higher severity of illness. Early administration of corticosteroids improved survival in non-mechanically ventilated patients; decreased ICU stay and may have prevented intubation.
Nest records, Nest Site selection ofGyps bengalensisWhite-rumped Vulture and the role of Feeding Station in Kangra, Himachal Pradesh
Authors: Sehgal Archi , Kumar Krishan , Rajan Rubina , Hore Upmanyu
Published: July 2020

Active nests ofGyps bengalensisWhite-rumped Vulture depends on elevation and aspects for nest site selection, while feeding station plays a significant role for determining the position of the nesting sites.This study attempted to record nest count for the breeding period 2018, identify key variables for the nest site selection and understand the role of feeding station in the nest site selection. Nest counts were conducted during the breeding period, each nest was categorized into active and inactive nest based on assesment of different components. Simultaneously, different variables (tree height, tree species, elevation and aspect) were recorded for each nest. Aerial distance was used to determine the role of feeding station for selecting the nesting sites. From the 24 nesting sites, 352 active nests were recorded, and a significant Pearson’s correlation for elevation and aspect were drawn. We found, vulture prefer single tree species for nesting. We also found that, 71% (n = 17) nesting sites located within radial distance of 20 km of the feeding station. High congregration of active nests within short radial distance from feeding station, signify the positive impact of management of feeding station by the wildlife wing of Forest department since 2008, for the ex-situ conservation of critically endangeredGyps bengalensisWhite-rumped Vulture
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes
Authors: Yao Guocai , Zhang Wenliang , Yang Minglei , Yang Huan , Wang Jianbo , Zhang Haiyue , Wei Lai , Xie Zhi , Li Weizhong
Published: July 2020

Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available throughhttp://www.liwzlab.cn/microphenodbandhttp://lilab2.sysu.edu.cn/microphenodb.