bluuebunny/crossref_metadata_2025 huggingface dataset:
Testing out of quarantine
Authors: McGowan Lucy D’Agostino , Lee Elizabeth C. , Grantz Kyra H. , Kucirka Lauren M. , Gurley Emily S. , Lessler Justin
Published: February 2021

Since SARS-CoV-2 emerged, a 14-day quarantine has been recommended based on COVID-19”s incubation period. Using an RT-PCR or rapid antigen test to “test out” of quarantine is a frequently proposed strategy to shorten duration without increasing risk. We calculated the probability that infected individuals test negative for SARS-CoV-2 on a particular day post-infection and remain symptom free for some period of time. We estimate that an infected individual has a 20.1% chance (95% CI 9.8-32.6) of testing RT-PCR negative on day five post-infection and remaining asymptomatic until day seven. We also show that the added information a test provides decreases as we move further from the test date, hence a less sensitive test that returns rapid results is often preferable to a more sensitive test with a delay.
Targeted screening for Alzheimer’s disease clinical trials using data-driven disease progression models
Authors: Oxtoby Neil P. , Shand Cameron , Cash David M. , Alexander Daniel C. , Barkhof Frederik ,   for the Alzheimer’s Disease Neuroimaging Initiative,   the Alzheimer’s Disease Cooperative Study
Published: February 2021

Heterogeneity in Alzheimer’s disease progression contributes to the ongoing failure to demonstrate efficacy of putative disease-modifying therapeutics that have been trialled over the past two decades. Any treatment effect present in a subgroup of trial participants (responders) can be diluted by non-responders who ideally should have been screened out of the trial. How to identify (screen-in) the most likely potential responders is an important question that is still without an answer. Here we pilot a computational screening tool that leverages recent advances in data-driven disease progression modelling to improve stratification. This aims to increase the sensitivity to treatment effect by screening out non-responders, which will ultimately reduce the size, duration, and cost of a clinical trial. We demonstrate the concept of such a computational screening tool by retrospectively analysing a completed double-blind clinical trial of donepezil in people with amnestic mild cognitive impairment (clinicaltrials.gov: NCT00000173), identifying a data-driven subgroup having more severe cognitive impairment who showed clearer treatment response than observed for the full cohort.
A mathematical model to estimate percentage secondary infections from margin of error of diagnostic sensitivity: Useful tool for regulatory agencies to assess the risk of propagation due to false negative outcome of diagnostics
Authors: Azhahianambi P , Karthik K , Aravindh Babu RP , Senthil kumar TMA , Balachandran C , Dhinakar Raj G
Published: February 2021

False negative outcome of a diagnosis is one the major reasons for the dissemination of the diseases with high risk of propagation. Diagnostic sensitivity and the margin of error determine the false negative outcome of the diagnosis. A mathematical model had been developed to estimate the mean % secondary infections based on the margin of error of diagnostic sensitivity, % prevalence and R0 value. This model recommends a diagnostic test with diagnostic sensitivity ≥ 96% and at least 92% lower bound limit of the 95% CI or ≤ 4% margin of error for a highly infectious diseases like COVID-19 to curb the secondary transmission of the infection due to false negative cases. Positive relationship was found between mean % secondary infection and margin of error of sensitivity suggesting greater the margin of error of a diagnostic test sensitivity, higher the number of secondary infections in a population due to false negative cases. Negative correlation was found between number of COVID-19 test kits (>90% sensitivity) with regulatory approval and margin of error (R= −0.92, p=0.023) suggesting lesser the margin of error of a diagnostic test, higher the chances of getting approved by the regulatory agencies. However, there are no specific regulatory standards available for margin of error of the diagnostic sensitivity of COVID-19 diagnostic tests. Highly infectious disease such as COVID-19, certainly need specific regulatory standards on margin of error or 95% CI of the diagnostic sensitivity to curb the dissemination of the disease due to false negative cases and our model can be used to set the standards such as sensitivity, margin of error or lower bound limit of 95% CI.
Neptune: An environment for the delivery of genomic medicine
Authors: Venner Eric , Yi Victoria , Murdock David , Kalla Sara E. , Wu Tsung-Jung , Sabo Aniko , Li Shoudong , Meng Qingchang , Tian Xia , Murugan Mullai , Cohen Michelle , Kovar Christie , Wei Wei-Qi , Chung Wendy K. , Weng Chunhua , Wiesner Georgia L. , Jarvik Gail P. , Muzny Donna , Gibbs Richard A. ,   eMERGE Consortium
Published: February 2021

Purpose

Genomic medicine holds great promise for improving healthcare, but integrating searchable and actionable genetic data into electronic health records remains a challenge. Here, we describe Neptune, a system for managing the interaction between a clinical laboratory and an electronic health record system.

Methods

We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis and EHR integration.

Results

Neptune enabled the analysis of data for generation of and delivery to EHR systems of over 15,000 clinical genomic reports. These projects demanded customizable clinical reports that contained a variety of genetic data types including SNVs, CNVs, pharmacogenomics and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow.

Conclusions

Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open and available athttps://gitlab.com/bcm-hgsc/neptune.
3-D optogenetic control of arteriole diameter in vivo
Authors: O’Herron Philip J. , Hartmann David A. , Xie Kun , Kara Prakash , Shih Andy Y.
Published: February 2021

Modulation of brain arteriole diameter is critical for maintaining cerebral blood pressure and controlling regional hyperemia during neural activity. However, studies of hemodynamic function in health and disease have lacked a method to control arteriole diameter independently with high spatiotemporal resolution. Here, we describe an all-optical approach to manipulate and monitor brain arteriole contractility in 3-dimensions using combined in vivo two-photon optogenetics and imaging. The expression of the red-shifted excitatory opsin, ReaChR, in vascular smooth muscle cells enabled rapid and repeated vasoconstriction controlled by brief light pulses. Two-photon activation of ReaChR using a spatial light modulator produced highly localized constrictions when targeted to individual arterioles within the neocortex. We demonstrate the utility of this method for examining arteriole contractile dynamics and creating transient focal blood flow reductions. Additionally, we show that optogenetic constriction can be used to reshape vasodilatory responses to sensory stimulation, providing a valuable tool to dissociate blood flow changes from neural activity.
Integrative phenotypic and genomic analyses reveal strain-dependent responses to acute ozone exposure and their associations with airway macrophage transcriptional activity
Authors: Tovar Adelaide , Crouse Wesley L. , Smith Gregory J. , Thomas Joseph M. , Keith Benjamin P. , McFadden Kathryn M. , Moran Timothy P. , Furey Terrence S. , Kelada Samir N. P.
Published: February 2021

Acute ozone (O3) exposure is associated with multiple adverse cardiorespiratory outcomes, the severity of which varies across human populations and rodent models from diverse genetic backgrounds. However, molecular determinants of response, including biomarkers that distinguish which individuals will develop more severe injury and inflammation (i.e., high responders), are poorly characterized. Here, we exposed adult, female and male mice from 6 strains, including 5 Collaborative Cross (CC) strains, to filtered air (FA) or 2 ppm O3for 3 hours, and measured several inflammatory and injury parameters 21 hours later. Additionally, we collected airway macrophages and performed RNA-seq analysis to investigate influences of strain, treatment, and strain-by-treatment interactions on gene expression as well as transcriptional correlates of lung phenotypes. Animals exposed to O3developed airway neutrophilia and lung injury, with varying degrees of severity. We identified many genes that were altered by O3exposure across all strains, and examination of genes whose expression was influenced by strain-by-treatment interactions revealed prominent differences in response between the CC017/Unc and CC003/Unc strains, which were low- and high-responders, respectively (as measured by cellular inflammation and injury). Further investigation of this contrast indicated that baseline gene expression differences likely contribute to their divergent post-O3exposure transcriptional responses. We also observed alterations in chromatin accessibility that differed by strain and with strain-by-treatment interactions, lending further plausibility that baseline differences can modulate post-exposure responses. Together, these results suggest that aspects of the respiratory response to O3exposure may be mediated through altered airway macrophage transcriptional signatures, and further confirms the importance of gene-by-environment interactions in mediating differential responsiveness to environmental agents.
Family dynamics reveal that female house mice preferentially breed in their maternal community
Authors: Evans Julian C. , Lindholm Anna K. , König Barbara
Published: February 2021

Whether females breed in their natal group is an important factor in the evolution of extended families in animal sociality. Breeding in natal groups comes with clear costs and benefits, depending on size of the group and presence of older relatives, including mothers. Studying individual decisions about whether to stay or leave can provide insight into the mechanisms and trade-offs governing the formation and structure of family groups. We investigated the family dynamics of a large population of free-ranging commensal house mice. Using dynamic community detection on long term datasets, we determined which females first bred in their natal group. We then looked at how this influenced breeding success. We found most females (77%) exhibited strong philopatry, breeding in their natal groups. Whether a female bred elsewhere was only predictable when natal groups were extremely small and related or large and unrelated. Despite this preference, breeding elsewhere made no difference in how quickly and successfully a female bred. However, presence of their mother did lead females to breed sooner when born during high breeding activity, when competition over reproduction is high. Based on these results, potential loss of fitness does not seem to be the main driver of philopatry in female house mice. The effect of the presence of mothers may indicate retaining prior social connections is an important benefit of breeding in the natal group. Mothers providing benefits also suggests lack of conflict between generations, which is likely an important attribute in the development of extended family groups.

Lay summary

Whether animals breed in the group they are born in influences how they form extended family groups. Whether females stay will depend on properties such as presence of older relatives, including mothers. Using long-term wild mouse data, we track groups and which group females bred in. Most stayed, but leaving didn’t reduce breeding success. Presence of mother, who generally stayed, did lead to earlier breeding. This might be a key advantage to remaining to breed.
GraphUnzip: unzipping assembly graphs with long reads and Hi-C
Authors: Faure Roland , Guiglielmoni Nadège , Flot Jean-François
Published: February 2021

Long reads and Hi-C have revolutionized the field of genome assembly as they have made highly continuous assemblies accessible for challenging genomes. As haploid chromosome-level assemblies are now commonly achieved for all types of organisms, phasing assemblies has become the new frontier for genome reconstruction. Several tools have already been released using long reads and/or Hi-C to phase assemblies, but they all start from a linear sequence, and are ill-suited for non-model organisms with high levels of heterozygosity. We present GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploidEscherichia coligenome, and on two real datasets for the genomes of the rotiferAdineta vagaand the potatoSolanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.
Gut regulates brain synaptic assembly through neuroendocrine signaling pathway
Authors: Shi Yanjun , Qin Lu , Shao Zhiyong
Published: February 2021

The gut-brain axis plays an essential role in regulating neural development in response to environmental stimuli, such as microbes or nutrients. Defects in gut-brain communication can lead to various neurological disorders. However, it remains unknown whether gut plays any intrinsic role in regulating neuronal development. Through a genetic screen inC. elegans, we uncovered that an intrinsic Wnt-endocrine pathway in gut regulates synaptic development and neuronal activity in brain. Specifically, the Wnt signaling upregulates the expression of the neuropeptide NLP-40 in the gut, which then facilitates presynaptic assembly through the neuronal expressed GPCR AEX-2 receptor during development. The NLP-40 acts most likely through modulating neuronal activity and promoting synaptic protein trafficking. Therefore, this study reveals a novel role of gut in synaptic development in the brain.
The Functional Order (FunOrder) tool – Identification of essential biosynthetic genes through computational molecular co-evolution
Authors: Vignolle Gabriel A. , Schaffer Denise , Mach Robert L. , Mach-Aigner Astrid R. , Derntl Christian
Published: February 2021

Secondary metabolites (SMs) are a vast group of compounds with different structures and properties. Humankind uses SMs as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs but they have problems with distinguishing essential genes from gap genes and defining the borders of a BGC. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or co-expression analyses. In this study, we developed a novel tool that allows automated identification of essential genes in a BGC based solely on genomic data. The Functional Order (FunOrder) tool – Identification of essential biosynthetic genes through computational molecular co-evolution – searches for co-evolutionary linked genes in the BGCs. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs, including antibiotics and other pharmaceuticals.
Chronic nicotine increases midbrain dopamine neuron activity and biases individual strategies towards reduced exploration in a foraging task
Authors: Dongelmans Malou , Durand-de Cuttoli Romain , Nguyen Claire , Come Maxime , Duranté Etienne K. , Lemoine Damien , Britto Raphael , Yahia Tarek Ahmed , Mondoloni Sarah , Didienne Steve , Bousseyrol Elise , Hannesse Bernadette , Reynolds Lauren M. , Torquet Nicolas , Dalkara Deniz , Marti Fabio , Mourot Alexandre , Naudé Jérémie , Faure Philippe
Published: February 2021

Long-term exposure to nicotine alters brain circuits and induces profound changes in decision-making strategies, affecting behaviors both related and unrelated to drug seeking and consumption. Using an intracranial self-stimulation reward-based foraging task, we investigated the impact of chronic nicotine on the trade-off between exploitation and exploration, and the role of ventral tegmental area (VTA) dopamine (DA) neuron activity in decision-making unrelated to nicotine-seeking. Model-based and archetypal analysis revealed a substantial inter-individual variability in decision-making strategies, with mice passively exposed to chronic nicotine visiting more frequently options associated with higher reward probability and therefore shifting toward a more exploitative profile compared to non-exposed animals. We then mimicked the effect of chronic nicotine on the tonic activity of VTA DA neurons using optogenetics, and found that photo-stimulated mice had a behavioral phenotype very close to that of mice exposed to nicotine, suggesting that the dopaminergic control of the exploration/exploitation balance is altered under nicotine exposure. Our results thus reveal a key role of tonic midbrain DA in the exploration/exploitation trade-off and highlight a potential mechanism by which nicotine affects decision-making.
Fat and carbohydrate interact to potentiate food reward in healthy weight but not in overweight or obesity
Authors: Perszyk Emily E. , Hutelin Zach , Trinh Jessica , Kanyamibwa Arsene , Fromm Sophie , Davis Xue S. , Wall Kathryn M. , Flack Kyle D. , DiFeliceantonio Alexandra , Small Dana M.
Published: February 2021

Prior work suggests that actual, but not estimated, energy density drives the reinforcing value of food [1,2] and that energy from fat and carbohydrate can interact to potentiate reward [2]. Here we sought to replicate these findings in an American sample and to determine if the effects are influenced by body mass index (BMI). Thirty participants with healthy weight (HW; BMI 21.92 ± 1.77;M±SD) and 30 participants with overweight/obesity (OW/OB; BMI 29.42 ± 4.44) rated pictures of common American snacks in 120-kcal portions for liking, familiarity, frequency of consumption, expected satiety, healthiness, energy content, energy density, and price. Participants then completed an auction task where they bid for the opportunity to consume each food. Snacks contained either primarily carbohydrate, primarily fat, or roughly equal portions of fat and carbohydrate (combo). Replicating prior work, we found that participants with HW bid the most for combo foods in linear mixed model analyses. This effect was not observed among individuals with OW/OB. Additionally, in contrast with previous reports [1,2], our linear regression analyses revealed a negative relationship between the actual energy density of the snacks and bid amount that was mediated by food price. Our findings support altered macronutrient reinforcement in obesity and highlight potential influences of the food environment on the regulation of food reward.
Mutagenesis of the Ammonium TransporterAcAmtReveals a Reproductive Role and a Novel Ammonia-Sensing Mechanism in the Malaria Vector MosquitoAnopheles coluzzii
Authors: Ye Zi , Liu Feng , Ferguson Stephen T. , Baker Adam , Pitts R. Jason , Zwiebel Laurence J.
Published: February 2021

Anopheline mosquitoes are the sole vectors of malaria and rely on olfactory cues for host seeking in which ammonia derived from human sweat plays an essential role. To investigate the function of theAnopheles coluzziiammonium transporter (AcAmt) in the mosquito olfactory system, we generated anAcAmtnull mutant line using CRISPR/Cas9.AcAmt-/-mutants displayed a series of novel phenotypes compared with wild-type mosquitoes including significantly lower insemination rates during mating and increased mortality during eclosion. Furthermore,AcAmt-/-males showed significantly lower sugar consumption whileAcAmt-/-females and pupae displayed significantly higher ammonia levels than their wild-type counterparts. Surprisingly, in contrast to previous studies inDrosophilathat revealed that the mutation of the ammonium transporter (DmAmt) induces a dramatic reduction of ammonia responses in antennal coeloconic sensilla, no significant differences were observed across a range of peripheral sensory neuron responses to ammonia and other odorants between wild-type andAcAmt-/-females. Taken together, these data support the existence of a unique ammonia-sensing mechanism in mosquitoes and that the ammonium transporter may be an important molecular target for vector control.

Key Messages

Mutagenesis ofAn. coluzziiammonium transporterAcAmtfollowed by comprehensive electrophysiological investigation suggest a novel ammonia-sensing pathway inAnophelesmosquitoes.

AcAmt-/-mutants displayed significant deficiencies in reproduction and eclosion, which are likely due to elevated ammonia levels and reduced ability of sugar feeding.

An. coluzziicoeloconic sensilla primarily detect amines and acids.
Deciphering active prophages from metagenomes
Authors: Kieft Kristopher , Anantharaman Karthik
Published: February 2021

Temperate phages (prophages) are ubiquitous in nature and persist as dormant components of host cells (lysogenic stage) before activating and lysing the host (lytic stage). Actively replicating prophages contribute to central community processes, such as enabling bacterial virulence, manipulating biogeochemical cycling, and driving microbial community diversification. Recent advances in sequencing technology have allowed for the identification and characterization of diverse phages, yet no approaches currently exist for identifying if a prophage has activated. Here, we present PropagAtE (Prophage Activity Estimator), an automated software tool for estimating if a prophage is in the lytic or lysogenic stage of infection. PropagAtE uses statistical analyses of prophage-to-host read coverage ratios to decipher actively replicating prophages, irrespective of whether prophages were induced or spontaneously activated. We demonstrate that PropagAtE is fast, accurate and sensitive, regardless of sequencing depth. Application of PropagAtE to prophages from 348 complex metagenomes from human gut, murine gut and soil environments identified distinct spatial and temporal prophage activation signatures, with the highest proportion of active prophages in murine gut samples. Among the soil habitats evaluated (bog, fen and palsa), we identified unique populations of Myxococcales, Acetobacteraceae and Acidimicrobiaceae prophages to be active in fen, palsa and bog habitats, respectively. Within the human gut, 11 prophage populations, some encoding the sulfur metabolism gene cysH or a rhuM-like virulence factor, were consistently present over time but not active. Overall, PropagAtE will facilitate accurate representations of viruses in microbiomes by associating prophages with their active roles in shaping microbial communities in nature.
Whole-genome analysis ofde novoand polymorphic retrotransposon insertions in Autism Spectrum Disorder
Authors: Borges-Monroy Rebeca , Chu Chong , Dias Caroline , Choi Jaejoon , Lee Soohyun , Gao Yue , Shin Taehwan , Park Peter J. , Walsh Christopher A. , Lee Eunjung Alice
Published: February 2021

Retrotransposons are dynamic forces in evolutionary genomics and have been implicated as causes of Mendelian disease and hereditary cancer, but their role in Autism Spectrum Disorder (ASD) has never been systematically defined. Here, we report 86,154 polymorphic retrotransposon insertions including >60% not previously reported and 158de novoretrotransposition events identified in whole genome sequencing (WGS) data of 2,288 families with ASD from the Simons Simplex Collection (SSC). As expected, the overall burden ofde novoevents was similar between ASD individuals and unaffected siblings, with 1de novoinsertion per 29, 104, and 192 births for Alu, L1, and SVA respectively, and 1de novoinsertion per 20 births total, while the location of transposon insertions differed between ASD and unaffected individuals. ASD cases showed morede novoL1 insertions than expected in ASD genes, and we also foundde novointronic retrotransposition events in known syndromic ASD genes in affected individuals but not in controls. Additionally, we observed exonic insertions in genes with a high probability of being loss-of-function intolerant, including a likely causative exonic insertion inCSDE1, only in ASD individuals. Althoughde novoretrotransposition occurs less frequently than single nucleotide and copy number variants, these findings suggest a modest, but important, impact of intronic and exonic retrotransposition mutations in ASD and highlight the utility of developing specific bioinformatic tools for high-throughput detection of transposable element insertions.
DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization
Authors: Green Harrison , Durrant Jacob D.
Published: February 2021

1

Lead optimization, a critical step in early-stage drug discovery, involves making chemical modifications to a small-molecule ligand to improve its drug-like properties (e.g., binding affinity). We recently developed DeepFrag, a deep-learning model capable of recommending such modifications. Though a powerful hypothesis-generating tool, DeepFrag is currently implemented in Python and so requires a certain degree of computational expertise. To encourage broader adoption, we have created the DeepFrag browser app, which provides a user-friendly graphical user interface that runs the DeepFrag model in users’ web browsers. The browser app does not require users to upload their molecular structures to a third-party server, nor does it require the separate installation of any third-party software. We are hopeful that the app will be a useful tool for both researchers and students. It can be accessed free of charge, without requiring registration, athttp://durrantlab.com/deepfrag. The source code is also available athttp://git.durrantlab.com/jdurrant/deepfrag-app, released under the terms of the open-source Apache License, Version 2.0.
Aperiodic measures of neural excitability are associated with anticorrelated hemodynamic networks at rest: a combined EEG-fMRI study
Authors: Jacob Michael S. , Roach Brian J. , Sargent Kaia , Mathalon Daniel H. , Ford Judith M.
Published: February 2021

The hallmark of resting EEG spectra are distinct rhythms emerging from a broadband, aperiodic background. This aperiodic neural signature accounts for most of total EEG power, although its significance and relation to functional neuroanatomy remains obscure. We hypothesized that aperiodic EEG reflects a significant metabolic expenditure and therefore might be associated with the default mode network while at rest. During eyes-open, resting-state recordings of simultaneous EEG-fMRI, we find that aperiodic and periodic components of EEG power are only minimally associated with activity in the default mode network. However, a whole-brain analysis identifies increases in aperiodic power correlated with hemodynamic activity in an auditory-salience-cerebellar network, and decreases in aperiodic power are correlated with hemodynamic activity in prefrontal regions. Desynchronization in residual alpha and beta power is associated with visual and sensorimotor hemodynamic activity, respectively. These findings suggest that resting-state EEG signals acquired in an fMRI scanner reflect a balance of top-down and bottom-up stimulus processing, even in the absence of an explicit task.

HIGHLIGHTS

Periodic and aperiodic EEG parameters associated with distinct resting-state networks

Increases in aperiodic power associated with an auditory-salience-cerebellar network

Decreases in aperiodic power associated with prefrontal regions

Global neural excitability may reflect stimulus processing or arousal attributable to the uniqueness of the resting-state MR-scanner environment
Water as a reactant in the first step of triosephosphate isomerase catalysis
Authors: Yates Max , Callis Patrik R.
Published: February 2021

The enzyme triosephosphate isomerase (TIM) performs a crucial role in the extraction of energy from glucose, doing so by converting dihydroxyacetone phosphate (DHAP) into glyceraldehyde phosphate, thereby doubling the yield of ATP molecules during glycolysis. The initial step of the mechanism is the seemingly unlikely abstraction of thepro-Rmethylene hydrogen from C1 by a conserved glutamate (Glu165), an assignment that has been both universally accepted yet a much-studied phenomenon for decades. In this work we introduce an alternative mechanism in which water as a strong general base abstracts the carbon proton acting effectively as hydroxide. We posit that strong electric fields associated with the substrate phosphate promote facile autoionization of water trapped near the phosphate dianion of DHAP and Glu165, an example of substrate assisted catalysis. Classical molecular dynamics simulations assert that the closest water oxygen atom is consistently closer to thepro-RH than the carboxylate oxygen atoms of the accepted base Glu165. Our proposal is further supported by quantum computations that confirm the implausibility of abstraction of the methylene hydrogen by glutamate and the ease with which it is abstracted by hydroxide. The necessity of Glu165 for efficient catalysis is attributed to its crucial involvement in trapping the vital water in an environment of high electric fields which promote ionization far more rapidly than in bulk solvent.
PATO: Pangenome Analysis Toolkit
Authors: Fernández-de-Bobadilla Miguel D. , Talavera-Rodríguez Alba , Chacón Lucía , Baquero Fernando , Coque Teresa M. , Lanza Val F.
Published: February 2021

Motivation

Comparative genomics is a growing field but one that will be eventually overtaken by sample size studies and the increase of available genomes in public databases. We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.

Results

PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20–30x times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Lastly, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.

Availability

The source code for PATO is freely available athttps://github.com/irycisBioinfo/PATOunder the GPLv3 license.

Contact

val.fernandez@salud.madrid.org

Supplementary information

Supplementary data are available at Bioinformatics online
Larval zebrafish display dynamic learning of aversive stimuli in a constant visual surrounding
Authors: Xu Jiale , Casanave Romelo , Guo Su
Published: February 2021

Balancing exploration and anti-predation are fundamental to the fitness and survival of all animal species from early life stages. How these basic survival instincts drive learning remains poorly understood. Here, employing a light/dark preference paradigm with well-controlled luminance history and constant visual surrounding in larval zebrafish, we analyzed intra- and inter-trial dynamics for two behavioral components, dark avoidance and center avoidance. We uncover that larval zebrafish display short-term learning of dark avoidance with initial sensitization followed by habituation; they also exhibit long-term learning that is sensitive to trial interval length. We further show that such stereotyped learning patterns is stimulus specific, as they are not observed for center avoidance. Finally, we demonstrate at individual levels that long-term learning is under homeostatic control. Together, our work has established a novel paradigm to understand learning, uncovered sequential sensitization and habituation, and demonstrated stimulus specificity, individuality, as well as dynamicity in learning.
Surviving hypothermia by ferritin-mediated iron detoxification
Authors: Pekec Tina , Lewandowski Jaroslaw , Komur Alicja A. , Sobanska Daria , Guo Yanwu , Świtońska-Kurkowska Karolina , Frankowski Marcin , Figiel Maciej , Ciosk Rafal
Published: February 2021

How animals rewire cellular programs to survive cold is a fascinating problem with potential biomedical implications, ranging from emergency medicine to space travel. Studying a hibernation-like response in the free-living nematodeCaenorhabditis elegans, we uncovered a regulatory axis that enhances the natural resistance of nematodes to severe cold. This axis involves conserved transcription factors, DAF-16/FoxO and PQM-1, which jointly promote cold survival by upregulating FTN-1, a protein related to mammalian Fth1/ferritin. Moreover, we show that inducing expression of Fth1 also promotes cold survival of mammalian neurons, a cell type particularly sensitive to deterioration in hypothermia. Our findings in both animals and cells suggest that FTN-1/Fth1 facilitates cold survival by detoxifying ROS-generating iron species. We finally show that mimicking the effects of FTN-1/Fth1 with drugs protects neurons from cold-induced degeneration, opening a potential avenue to improved treatments of hypothermia.
Genome-scale CRISPR screening in a single mouse liver
Authors: Keys Heather R. , Knouse Kristin A.
Published: February 2021

A complete understanding of the genetic determinants underlying mammalian physiology and disease is limited by the availability of tools for high-throughput genetic dissection in the living organism. Genome-wide screening using CRISPR-Cas9 has emerged as a powerful method for uncovering the genetic regulation of cellular processes, but the need to stably deliver single guide RNAs to millions of cells has largely restricted its implementation toex vivosystems. There thus remains a pressing need for accessible high-throughput functional genomics in a living organism. Here, we establish genome-wide enrichment and depletion screening in the liver of a single mouse and use this approach to uncover the complete regulation of cellular fitness in a living organism. We uncover regulation of cell fitness not previously identified in cell culture screens, underscoring the power of bringing high-throughput functional genomics into the organism. The approach we developed is accessible, robust, scalable, and adaptable to diverse phenotypes and CRISPR applications. We have hereby established a foundation for high-throughput functional genomics in a living mammal, enabling unprecedented insight into physiology and disease.
A gene expression platform to predict benefit from adjuvant external beam radiation in resected non-small cell lung cancer
Authors: Ahmed Kamran A. , Creelan Ben C. , Peacock Jeffrey , Mellon Eric A , Kim Youngchul , Grass G. Daniel , Perez Bradford A , Rosenberg Stephen A. , Dilling Thomas J. , Eschrich Steven A. , Chiappori Alberto A. , Torres-Roca Javier F.
Published: February 2021

Background

We hypothesized that the radiosensitivity index (RSI), would classify non-small cell lung cancer (NSCLC) patients into radioresistant (RR) or radiosensitive (RS).

Methods

We identified resected pathologic stage III NSCLC. For the radiation group (RT) group, at least 45 Gy of external beam radiation was required. mRNA was extracted from primary tumor. The predefined cut-point was the median RSI with a primary endpoint of local control. Similar criteria were then applied to two extramural datasets (E1; E2) with progression free survival as the primary endpoint.

Results

Median follow-up from diagnosis was 23.5 months (range: 4.8-169.6 months). RSI was associated with time to local failure in the RT group with a two-year rate of local control of 80% and 56% between RS and RR groups, respectively p=0.02. RSI was the only variable found to be significant on Cox local control analysis (HR 2.9; 95% CI: 1.2-8.2; p=0.02). There was no significance of RSI in predicting local control in patients not receiving RT, p=0.48. A cox regression model between receipt of radiotherapy and RSI combining E1 and E2 showed that the interaction term was significant for PFS (3.7; 95% CI 1.4-10; p=0.009). A summary measure combining E1 and E2 showed statistical significance for PFS between RR and RS patients treated with radiotherapy (HR 2.7l; 95% CI 1.3-5.6; p=0.007) but not in patients not treated with radiotherapy (HR 0.94; 95% CI 0.5-1.78; p=0.86).

Conclusions

RSI appears to be predictive for benefit from adjuvant radiation. Prospective validation is required.
Molecular profiling of retinal pigment epithelial cell differentiation for therapeutic use
Authors: Petrus-Reurer Sandra , Lederer Alex R. , Baqué-Vidal Laura , Douagi Iyadh , Pannagel Belinda , Aronsson Monica , Bartuma Hammurabi , Wagner Magdalena , André Helder , Sundström Erik , Bhaduri Aparna , Kriegstein Arnold , Kvanta Anders , Manno Gioele La , Lanner Fredrik
Published: February 2021

Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, detailed single cell mapping of the transient cellular and molecular dynamics from the pluripotent state to mature RPE has not been performed. Here we conduct single-cell transcriptomic analyses of 25,718 cells during differentiation as well as in embryonic and adult retina references, revealing differentiation progression through an un-expected initial cell diversification recapitulating early embryonic development before converging towards an RPE lineage. We also identified NCAM1 to track and capture an intermediate retinal progenitor with the potential to give rise to multiple neuroepithelial lineages. Finally, we profiled hESC-RPE cells after subretinal transplantation into the rabbit eye, uncovering robustin vivomaturation towards an adult state. Our detailed evaluation of hESC-RPE differentiation supports the development of safe and efficient pluripotent stem cell-based therapies for AMD.
Cortical Processing of Arithmetic and Simple Sentences in an Auditory Attention Task
Authors: Kulasingham Joshua P. , Joshi Neha H. , Rezaeizadeh Mohsen , Simon Jonathan Z.
Published: February 2021

Cortical processing of arithmetic and of language rely on both shared and task-specific neural mechanisms, which should also be dissociable from the particular sensory modality used to probe them. Here, spoken arithmetical and non-mathematical statements were employed to investigate neural processing of arithmetic, compared to general language processing, in an attention-modulated cocktail party paradigm. Magnetoencephalography (MEG) data was recorded from 22 subjects listening to audio mixtures of spoken sentences and arithmetic equations while selectively attending to one of the two speech streams. Short sentences and simple equations were presented diotically at fixed and distinct word/symbol and sentence/equation rates. Critically, this allowed neural responses to acoustics, words, and symbols to be dissociated from responses to sentences and equations. Indeed, the simultaneous neural processing of the acoustics of words and symbols was observed in auditory cortex for both streams. Neural responses to sentences and equations, however, was predominantly to the attended stream, and originated primarily from left temporal, and parietal areas, respectively. Additionally, these neural responses were correlated with behavioral performance in a deviant detection task. Source-localized Temporal Response Functions revealed distinct cortical dynamics of responses to sentences in left temporal areas and equations in bilateral temporal, parietal and motor areas. Finally, the target of attention could be decoded from MEG responses, especially in left superior parietal areas. In short, the neural responses to arithmetic and language are especially well segregated during the cocktail party paradigm, and the correlation with behavior suggests that they may be linked to successful comprehension or calculation.

Significance Statement

Neural processing of arithmetic relies on dedicated, modality independent cortical networks that are distinct from those underlying language processing. Using a simultaneous cocktail party listening paradigm, we found that these separate networks segregate naturally when listeners selectively attend to one type over the other. Time-locked activity in the left temporal lobe was observed for responses to both spoken sentences and equations, but the latter additionally showed bilateral parietal activity consistent with arithmetic processing. Critically, these responses were modulated by selective attention and correlated with task behavior, consistent with reflecting high-level processing for speech comprehension or correct calculations. The response dynamics show task-related differences that were used to reliably decode the attentional target of sentences or equations.
Dendritic domain-specific sampling of long-range axons shapes feedforward and feedback connectivity of L5 neurons
Authors: Galloni Alessandro R. , Ye Zhiwen , Rancz Ede
Published: February 2021

Feedforward and feedback pathways interact in specific dendritic domains to enable cognitive functions such as predictive processing and learning. Based on axonal projections, hierarchically lower areas are thought to form synapses primarily on dendrites in middle cortical layers, while higher-order areas are posited to target dendrites in layer 1 and in deep layers. However, the extent to which functional synapses form in regions of axo-dendritic overlap has not been extensively studied. Here, we use viral tracing in the secondary visual cortex of mice to map brain-wide inputs to thick-tufted layer 5 pyramidal neurons. Furthermore, we provide a comprehensive map of input locations through subcellular optogenetic circuit mapping. We show that input pathways target distinct dendritic domains with far greater specificity than appears from their axonal branching, often deviating substantially from the canonical patterns. Common assumptions regarding the dendrite-level interaction of feedforward and feedback inputs may thus need revisiting.
Expression of Cloned Genes in E. coli Using IPTG-Inducible Promoters
Authors: Kielkopf Clara L. , Bauer William , Urbatsch Ina L.
Published: February 2021

Many Escherichia coli expression vectors make use of the lac operon. In general, the lac operator (lacO) is located downstream from the promoter of the target gene, so that binding of the lac repressor blocks transcription initiation until lactose or the isopropyl-β-d-thiogalactopyranoside (IPTG) analog is added. The protocol given here is intended for use with IPTG-inducible vectors. l-Arabinose-inducible systems derived from the ara operon offer an alternative to expression systems based on the lac operon; guidance for their use is also provided.
Preparation of Cell Extracts for Purification of Soluble Proteins Expressed in E. coli
Authors: Kielkopf Clara L. , Bauer William , Urbatsch Ina L.
Published: February 2021

Recovery of intracellular proteins requires disruption of the host cell before the target protein is extracted and isolated. For cells enveloped in cell walls (such as Escherichia coli), vigorous methods are often required. This protocol focuses on E. coli lysis by sonication. Also included are methods for lysis by freeze–thaw and enzymatic treatments.
Hierarchy in America
Authors: KEELER WARD
Published: February 2021

Religious commitment, support for the military and free‐market capitalism, and aversion to the welfare system, homosexuality and ‘big government’ are all attitudes widely shared among conservative Americans. Apparently unrelated, these views reflect an unrecognized but real ideological embrace of hierarchical understandings: to wit, power comes from above, exchange relations with powerful entities are the means for bettering one's circumstances and such relations are predicated on differences among parties. God, military and political leaders and the captains of industry all constitute personalized nodes of power to whom subordinating oneself offers chances for advancement. Government, by way of contrast, constitutes an impersonal force liable only to take someone's liberty and money and give no return. Adherence to hierarchical assumptions explains support for illiberal leaders in the US and beyond.
Processes Underlying Interfirm Cooperation
Authors: Lahiri Somnath , Kundu Sumit , Munjal Surender
Published: February 2021

This special issue intended to bring together scholarly insights on the processes that underlie the formation, growth, management and termination of interfirm cooperation (IFC). In this introductory paper, we highlight what we know about IFC and why fresh perspectives are warranted on this phenomenon from a conceptual and practical standpoint. We also highlight the contribution of each paper published in this special issue. The seven selected papers differ in their theoretical perspective, context, research methodology and findings, but collectively they enhance our understanding of various IFC processes. We end this paper by highlighting fertile avenues of future research.
The effects of function‐based communication intervention for a student with emotional disturbance in a general education setting
Authors: Perihan Celal , Bicer Ali
Published: February 2021

Research has shown that most children with emotional disturbance (ED) are struggling to use communication skills and they may tend to use inappropriate behaviours as a form of communication to disclose their needs. A function‐based communication intervention might be an effective approach to decrease inappropriate behaviours of children with ED. The purpose of this single‐case multiple baseline reversal design (ABAB) study was to examine the effectiveness of the function‐based communication intervention for on‐task and disruptive behaviours of an 8‐year‐old student with ED. Functional behavioural assessment (FBA) was conducted and based on the findings of FBA, a colour‐coded communication system, was implemented during reading and math classes. The findings indicated that function‐based communication intervention was effective in increasing on‐task as well as decreasing disruptive behaviours. Furthermore, the function‐based communication intervention improved communication between the teacher and the student that resulted in decreasing disruptive behaviours in a general classroom setting. The generalisability of the findings due to the limited number of participants was an important limitation for this study. Future directions, as well as implications for practices, are discussed.