bluuebunny/crossref_metadata_2025 huggingface dataset:
Postimplementation Evaluation of a Machine Learning–Based Deterioration Risk Alert to Enhance Sepsis Outcome Improvements
Authors: Linnen Daniel T. , Hu Xiao , Stephens Caroline E.
Published: August 2020

Machine learning–based early warning systems (EWSs) can detect clinical deterioration more accurately than point-score tools. In patients with sepsis, however, the timing and scope of sepsis interventions relative to an advanced EWS alert are not well understood. The objectives of this study were to evaluate the timing and frequency of fluid bolus therapy, new antibiotics, and Do Not Resuscitate (DNR) status relative to the time of an advanced EWS alert. We conducted 2 rounds of chart reviews of patients with an EWS alert admitted to community hospitals of a large integrated health system in Northern California (round 1: n = 21; round 2: n = 47). We abstracted patient characteristics and process measures of sepsis intervention and performed summary statistics. Sepsis decedents were older and sicker at admission and alert time. Most EWS alerts occurred near admission, and most sepsis interventions occurred before the first alert. Of 14 decedents, 12 (86%) had a DNR order before death. Fluid bolus therapy and new intravenous antibiotics frequently occurred before the alert, suggesting a potential overlap between sepsis care in the emergency department and the first alert following admission. Two tactics to minimize alerts that may not motivate new sepsis interventions are (1) locking out the alert during the immediate time after hospital admission; and (2) triaging and reviewing patients with alerts outside of the unit before activating a bedside response. Some decedents may have been on a palliative/end-of-life trajectory, because DNR orders were very common among decedents. Nurse leaders sponsoring or leading machine learning projects should consider tactics to reduce false-positive and clinically meaningless alerts dispatched to clinical staff.
Ethics in the Pediatric Emergency Department: When Mistakes Happen
Authors: Dreisinger Naomi , Zapolsky Nathan
Published: August 2020

The emergency department (ED) is an environment that is conducive to medical errors. The ED is a time-pressured environment where physicians aim to rapidly evaluate and treat patients. Quick thinking and problem-based solutions are often used to assist in evaluation and diagnosis. Error analysis leads to an understanding of the cause of a medical error and is important to prevent future errors. Research suggests mechanisms to prevent medical errors in the pediatric ED, but prevention is not always possible. Transparency about errors is necessary to assure a trusting doctor-patient relationship. Patients want to be informed about all errors, and apologies are hard. Apologizing for a significant medical error that may have caused a complication is even harder. Having a systematic way to go about apologizing makes the process easier, and helps assure that the right information is relayed to the patient and his or her family. This creates an environment of autonomy and shared decision making that is ultimately beneficial to all aspects of patient care.
Atlantoaxial Rotatory Subluxation in Children
Authors: Powell Elizabeth C. , Leonard Jeffrey R. , Olsen Cody S. , Jaffe David M. , Anders Jennifer , Leonard Julie C.
Published: August 2020

Objectives

Pediatric cervical injuries are uncommon. This study was to describe injury circumstances, clinical findings, and management among children diagnosed with atlantoaxial rotatory subluxation (AARS) to aid in its recognition and management.

Methods

Subanalysis of a large case-control study from January 2000 to December 2004 in 17 hospitals in the Pediatric Emergency Care Applied Research Network was performed. Cases were children younger than 16 years with AARS after blunt trauma (n = 55); controls were (a) children with other cervical spine injuries (other CSI, n = 485) and (b) those with normal imaging of the cervical spine (non-CSI, n = 1060).

Results

Children with AARS were younger (mean [SD] age, 7.7 [3.8] vs 10.7 [4.6]; Wilcoxon P < 0.01). Falls accounted for 36% of injuries; there were no diving mechanisms (vs other CSI, falls 19%, Fisher exact P < 0.01, and diving 7%, P = 0.04). Children with AARS sought medical care more than 24 hours after the injury event (21% vs 1% for non-CSI controls, P < 0.01). Clinical findings associated with AARS included neck pain (67%) and torticollis (57%) versus other CSI, pain (47%) and torticollis (5%, P < 0.01) for each, and versus non-CSI controls, pain (33%) and torticollis (6%, P < 0.01) for each. Management of AARS included no intervention (n = 6, 11%), soft or rigid collar only (n = 24, 44%), traction (n = 14, 25%), halo (n = 9, 16%), internal fixation (n = 2, 4%), and varied across institutions (P = 0.02).

Conclusions

Children with AARS often have a delayed presentation with neck pain and torticollis; falls are a common injury mechanism. Treatment varied across institutions. Further work is needed to identify optimal management.
Vertical structure in chlorophyll profiles: influence on primary production in the Arctic Ocean
Authors: Bouman Heather A. , Jackson Thomas , Sathyendranath Shubha , Platt Trevor
Published: August 2020

Subsurface chlorophyll maximum (SCM) layers are prevalent throughout the Arctic Ocean under stratified conditions and are observed both in the wake of retreating sea ice and in thermally stratified waters. The importance of these layers on the overall productivity of Arctic pelagic ecosystems has been a source of debate. In this study, we consider the three principal factors that govern productivity within SCMs: the shape of the chlorophyll profile, the photophysiological characteristics of phytoplankton and the availability of light in the layer. Using the information on the biological and optical parameters describing the vertical structure of chlorophyll, phytoplankton absorption and photosynthesis–irradiance response curves, a spectrally resolved model of primary production is used to identify the set of conditions under which SCMs are important contributors to water-column productivity. Sensitivity analysis revealed systematic errors in the estimation of primary production when the vertical distribution of chlorophyll was not taken into account, with estimates of water-column production using a non-uniform profile being up to 97% higher than those computed using a uniform one. The relative errors were shown to be functions of the parameters describing the shape of the biomass profile and the light available at the SCM to support photosynthesis. Given that SCM productivity is believed to be largely supported by new nutrients, it is likely that the relative contribution of SCMs to new production would be significantly higher than that to gross primary production. We discuss the biogeochemical and ecological implications of these findings and the potential role of new ocean sensors and autonomous underwater vehicles in furthering the study of SCMs in such highly heterogeneous and remote marine ecosystems.

This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
Benthic-pelagic coupling in the Barents Sea: an integrated data-model framework
Authors: Freitas Felipe S. , Hendry Katharine R. , Henley Sian F. , Faust Johan C. , Tessin Allyson C. , Stevenson Mark A. , Abbott Geoffrey D. , März Christian , Arndt Sandra
Published: August 2020

The Barents Sea is experiencing long-term climate-driven changes, e.g. modification in oceanographic conditions and extensive sea ice loss, which can lead to large, yet unquantified disruptions to ecosystem functioning. This key region hosts a large fraction of Arctic primary productivity. However, processes governing benthic and pelagic coupling are not mechanistically understood, limiting our ability to predict the impacts of future perturbations. We combine field observations with a reaction-transport model approach to quantify organic matter (OM) processing and disentangle its drivers. Sedimentary OM reactivity patterns show no gradients relative to sea ice extent, being mostly driven by seafloor spatial heterogeneity. Burial of high reactivity, marine-derived OM is evident at sites influenced by Atlantic Water (AW), whereas low reactivity material is linked to terrestrial inputs on the central shelf. Degradation rates are mainly driven by aerobic respiration (40–75%), being greater at sites where highly reactive material is buried. Similarly, ammonium and phosphate fluxes are greater at those sites. The present-day AW-dominated shelf might represent the future scenario for the entire Barents Sea. Our results represent a baseline systematic understanding of seafloor geochemistry, allowing us to anticipate changes that could be imposed on the pan-Arctic in the future if climate-driven perturbations persist.

This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning’.
Analysis and prediction of Covid-19 spreading through Bayesian modelling with a case study of Uttar Pradesh, India
Authors: Deepmala  , Srivastava Nishant Kumar , Kumar Vineet , Singh Sanjay Kumar
Published: August 2020

The pandemic of coronavirus disease 2019 (COVID-19) started in Wuhan, China, and spread worldwide. In India, COVID-19 cases increased rapidly throughout India. Various measures like awareness program, social distancing, and contact tracing have been implemented to control the COVID-19 outbreak. In the absence of any vaccine, the prediction of the confirmed, deceased, and recovered cases is required to enhance the health care system’s capacity and control the transmission. In this study, the cumulative and daily confirmed, deceased, and recovered cases in Uttar Pradesh, India, were analyzed. We used the logistic and Gompertz non-linear regression model using a Bayesian paradigm. We build the prior distribution of the model using information obtained from some other states of India, which are already reached at the advanced stage of COVID-19. Results from the analysis indicated that the predicted maximum number of confirmed, deceased, and recovered cases will be around 1157335, 5843, and 1145829 respectively. The daily number of confirmed, deceased, and recovered cases will be maximum at 104th day, 73rd day, and 124th day from 16 June 2020. Further from this analysis we can conclude that the COVID-19 will be over probably by early-June, 2021. The analysis did not consider any changes in government control measures. We hope this study can provide some relevant information to the government and health officials.
Decline, and Regional Disparities, in Medical Cocaine Usage in the United States
Authors: Armbuster Youngeun C. , Banas Brian N. , Feickert Kristen D. , England Stephanie E. , Moyer Erik J. , Christie Emily L. , Chughtai Sana , Giuliani Tanya J. , Halden Rolf U. , McCall Kenneth L. , Piper Brian J.
Published: August 2020

Purpose

Cocaine is a stimulant with a complex history that is used in otorhinolaryngological surgeries as a local anesthetic and vasodilator. There is extensive regulation in the United States for the storage and disposal of this Schedule II drug, potentially incentivizing health care professionals to avoid use. This descriptive study characterized medical cocaine use in the United States.

Methods

Retail drug distribution from 2002-2017 in units of grams of weight was extracted for each state from the Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System database, which reports on medical, research, and analytical-chemistry use. The percent of buyers (hospitals, pharmacies, providers) was obtained. Use per state, corrected for population, was determined. Available data on cocaine use, as reported by the Medicare and Medicaid programs for 2013 – 2017, also were examined.

Results

Medical cocaine use in the US, measured on the basis of mass, decreased 62.5% from 2002 to 2017. Hospitals accounted for 84.9% and practitioners for 9.9% of cocaine distribution in 2017. The number of pharmacies nationwide carrying cocaine dropped by 69.4% to 206. The percent of all US hospitals, practitioners, and pharmacies that carried cocaine in 2017 was 38.4%, 2.3%, and 0.3%, respectively. There was a seven-fold difference in distribution per state in 2002 (South Dakota = 76.1 mg/100 persons, Delaware = 10.1 mg/100 persons). Similarly, there was a ten-fold regional disparity observed for 2017. Relative to the average state, those reporting the highest values (Montana = 20.1 and North Dakota = 24.1 mg/100 persons), were significantly elevated. Cocaine use within the Medicare and Medicaid programs was negligible.

Conclusion

Medical cocaine use across the United States exhibited a pronounced decline over a fifteen-year period. If this pattern continues, licit cocaine will soon become an obscure pharmacological relic of interest only to analytical chemists and medical historians.

Key Points

Question:How has medical use of cocaine, a local anesthetic and vasoconstrictor administered for otorhinolaryngological surgeries and some diagnostic procedures, changed in the United States?

Findings:Cocaine usage, as reported to the Drug Enforcement Administration has undergone a pronounced (62.5%) decline over the past fifteen-years, while some pronounced regional differences were noted.

Meaning:Although cocaine has played a key role in the history of anesthesia, the development of safer and non-controlled alternatives may continue to supplant this agent in contemporary use.
Lymphocyte subset alterations with disease severity, imaging manifestation, and delayed hospitalization in COVID-19 patients
Authors: Wu Daxian , Wu Xiaoping , Huang Jiansheng , Rao Qunfang , Zhang Qi , Zhang Wenfeng
Published: August 2020

Background

COVID-19 continuously threated public health heavily. Present study aimed to investigate the lymphocyte subset alterations with disease severity, imaging manifestation, and delayed hospitalization in COVID-19 patients.

Methods

Lymphocyte subsets was classified using flow cytometry with peripheral blood collected from 106 patients.

Results

Multivariate logistic regression showed that chest tightness, lymphocyte count, and γ-glutamyl transpeptidase were the independent predictors for severe COVID-19. The T cell, CD4+ T cell and B cell counts in severe patients were significantly lower than that in mild patients (p = 0.004, 0.003 and 0.046, respectively). Only the T cell count was gradually decreased with the increase of infiltrated quadrants of lesions in computed tomography (CT) (p = 0.043). The T cell, CD4+ T cell, and CD8+ T cell counts were gradually decreased with the increase of infiltrated area of the maximum lesion in CT (p = 0.002, 0.003, 0.028; respectively). The T cell count, as well as CD4+ T cell, CD8+ T cell, and NK cell counts were gradually decreased with the increased delayed hospitalization (p = 0.003, 0.002, 0.013, and 0.012; respectively). The proportion of T cell was gradually decreased but B cell was gradually increased with the increased delayed hospitalization (p = 0.031 and 0.003, respectively).

Conclusion

T cell and CD4+ T cell counts negatively correlated with disease severity, CT manifestation and delayed hospitalization. CD4+ T cell was mainstay of immunity response in COVID-19 patients.
Alcohol, calories and obesity: A rapid systematic review and meta-analysis of consumer knowledge, support and behavioural effects of energy labelling on alcoholic drinks
Authors: Robinson Eric , Humphreys Gabrielle , Jones Andrew
Published: August 2020

Mandatory energy (calorie) labelling of alcoholic drinks is a public health measure that could be used to address both alcohol consumption and obesity. We systematically reviewed studies examining consumer knowledge of the energy content of alcoholic drinks, public support for energy labelling and the effect of energy labelling of alcoholic drinks on consumption behaviour. Eighteen eligible studies (from 16 sources) were included. Among studies examining consumer knowledge of the energy content of alcoholic drinks (N=8) and support for energy labelling (N=9), there was moderate evidence that people tend to be unaware of the energy content of alcoholic drinks (pooled estimate: 74% [95% CIs 64-82%] of participants inaccurate estimating energy content) and support energy labelling (pooled estimate: 64% [95% CIs 53%-73% support policy]. Six studies examined the effect of energy labelling on consumer behaviour and findings were indicative of no likely effect of labelling. However, the majority of studies were of low methodological quality, used proxy outcome measures and none of the studies were conducted in real-world settings, resulting in a very low level of evidence. Further research is required to determine whether energy labelling of alcoholic drinks affects consumer behaviour and is likely to be an effective public health policy.
A comparison of Emergency Department presentations for Medically Unexplained Symptoms in Frequent Attenders during COVID-19
Authors: Daniels Natasha Faye , Ridwan Raiiq , Barnard Ed B G , Amanullah Talha Muneer , Hayhurst Catherine
Published: August 2020

Background

Medically Unexplained Symptoms (MUS) refer to symptoms with no identified organic aetiology, and are amongst the most challenging for patients and Emergency Department (ED) staff. Providers working in our ED perceived an increase in severity and frequency of these types of presentations during the COVID-19 pandemic.

Methods

A retrospective list of frequent attenders (FA) presenting five or more times to the ED between two 122-day periods were examined: 01 Mar to 30 Jun 2019 (Control) and 2020 (COVID-19). The FA group were then examined to identify patients presenting with MUS (FA-MUS). Data were analysed in Prism; presented as n(%), % (95% confidence interval (95%CI) – Wilson/Brown method). Proportions were compared with a two-tailed Fisher’s exact test. A Baptista-Pike odds ratio was used to estimate magnitude and precision.

Results

The total number of ED attendances during the control period was n=42,785 which reduced to n=28,806 in the COVID-19 period, a decrease of 32.7%. The control FA cohort had n=44 FA-MUS patients with 149 ED visits. This increased to n=65 FA-MUS patients with 267 visits during COVID-19, p=0.44. There was a significant increase in the proportion of all ED visits that were FA-MUS: 0.3% (control) compared to 0.9% (COVID-19); OR 2.7, p<0.001. There was a significant increase in shortness of breath amongst MUS during the COVID-19 pandemic relative to the control period (p<0.01), with no significant difference in any other MUS category.

Conclusion

Whilst the total number of ED attendances reduced by almost one third during COVID-19, the actual number of all visits by frequent attenders with MUS increased and the proportion of attendances by these tripled during the same period. This presents an increasing challenge to ED clinicians who may feel underprepared to manage these patients effectively.

What is already known

Medically Unexplained Symptoms (MUS) are those that have no identified organic aetiology - they are amongst the most challenging presentations for patients and Emergency Department (ED) staff.

During times of stress and uncertainty, frequent attenders (FA) appear to be disproportionately affected by MUS. However, there are few data examining the impact of COVID-19 on the FA population.

What this paper adds

There was a significant increase in the proportion of all ED visits by FAs during the first four months of the COVID-19 pandemic.

There was a significant increase in the proportion of all ED visits by FAs with MUS during the first four months of the COVID-19 pandemic.

The proportion of MUS presentations that were ‘shortness of breath’ was significantly higher in the COVID-19 period compared to the control period. There were no other proportional differences observed in MUS categories.
Effectiveness of Localized Lockdowns in the COVID-19 Pandemic
Authors: Li Yige , Undurraga Eduardo A. , Zubizarreta José R.
Published: August 2020

Non-pharmaceutical interventions, such as social distancing and lockdowns, have been essential to control the COVID-19 pandemic. In particular, localized lockdowns in small geographic areas have become an important policy intervention to prevent viral spread in cases of resurgence. These localized lockdowns can result in lower social and economic costs compared to larger-scale suppression strategies. Using an integrated dataset from Chile (March 3 through June 15, 2020) and a novel synthetic control approach, in this paper we estimate the effect of localized lockdowns, disentangling its direct and indirect causal effects on SARS-CoV-2 transmission. Our results show that the effects of localized lockdowns are strongly modulated by their duration and are influenced by indirect effects from neighboring geographic areas. Our estimates suggest that extending localized lockdowns can slow down the pandemic; however, localized lockdowns on their own are insufficient to control pandemic growth in the presence of indirect effects from contiguous neighboring areas that do not have lockdowns. These results provide critical empirical evidence about the effectiveness of localized lockdowns in interconnected geographic areas.
WITHDRAWN: Rad5 and Rad51 act at telomeres through two partially distinct pathways
Authors: Henninger Erin E. , Jolivet Pascale , Berardi Prisca , Fallet Emilie , Benmounah Mohcen , Zeinoun Bechara , Charvin Gilles , Xu Zhou , Mattarocci Stefano , Teixeira Maria Teresa
Published: August 2020

Withdrawal Statement

The authors have withdrawn their manuscript because, upon reanalyzing the primary data it appears that the methods used by one of the authors, S.M., might have compromised the reliability of the data presented in Figure 1. We sincerely apologize for any harm or confusion this may cause to BioRxiv and its users.
Natural enemies have inconsistent impacts on the coexistence of competing species
Authors: Terry J. Christopher D. , Chen J. , Lewis O. T.
Published: August 2020

The role of natural enemies in promoting coexistence of competing species has generated substantial debate. Modern coexistence theory provides a detailed framework to investigate this topic, but there have been remarkably few empirical applications to the impact of natural enemies.

We tested experimentally the capacity for a generalist enemy to promote coexistence of competing insect species, and the extent to which any impact can be predicted by trade-offs between reproductive rate and susceptibility to natural enemies.

We used experimental mesocosms to conduct a fully-factorial pairwise competition experiment for six rainforestDrosophilaspecies, with and without a generalist pupal parasitoid. We then parameterised models of competition and examined the coexistence of each pair ofDrosophilaspecies within the framework of modern coexistence theory.

We found idiosyncratic impacts of parasitism on pairwise coexistence, mediated through changes in fitness differences, not niche differences. There was no evidence of an overall reproductive rate – susceptibility trade-off. Pairwise reproductive rate – susceptibility relationships were not useful shortcuts for predicting the impact of parasitism on coexistence.

Our results exemplify the value of modern coexistence theory in multi-trophic contexts and the importance of contextualising the impact of natural enemies. In the set of species investigated, competition was affected by the higher trophic level, but the overall impact on coexistence cannot be easily predicted just from knowledge of relative susceptibility. Methodologically, our Bayesian approach highlights issues with the separability of model parameters within modern coexistence theory and shows how using the full posterior parameter distribution improves inferences. This method should be widely applicable for understanding species coexistence in a range of systems.
Coordinated interactions between endothelial cells and macrophages in the islet microenvironment promote β cell regeneration
Authors: Saunders Diane C. , Aamodt Kristie I. , Richardson Tiffany M. , Hopkirk Alec , Aramandla Radhika , Poffenberger Greg , Jenkins Regina , Flaherty David K. , Prasad Nripesh , Levy Sean E. , Powers Alvin C. , Brissova Marcela
Published: August 2020

Endogenous β cell regeneration could alleviate diabetes, but proliferative stimuli within the islet microenvironment are incompletely understood. We previously found that β cell recovery following hypervascularization-induced β cell loss involves interactions with endothelial cells (ECs) and macrophages (MΦs). Here we show that proliferative ECs modulate MΦ infiltration and phenotype during β cell loss, and recruited MΦs are essential for β cell recovery. Furthermore, VEGFR2 inactivation in quiescent ECs accelerates islet vascular regression during β cell recovery and leads to increased β cell proliferation without changes in MΦ phenotype or number. Transcriptome analysis of β cells, ECs, and MΦs reveals that β cell proliferation coincides with elevated expression of extracellular matrix remodeling molecules and growth factors likely driving activation of proliferative signaling pathways in β cells. Collectively, these findings suggest a new β cell regeneration paradigm whereby coordinated interactions between intra-islet MΦs, ECs, and extracellular matrix mediate β cell self-renewal.
Using Neutralization Landscapes to enumerate Antibody Behavior and Decompose Antibody Mixtures
Authors: Einav Tal , Creanga Adrian , Andrews Sarah F. , McDermott Adrian B. , Kanekiyo Masaru
Published: August 2020

Antibodies constitute a key line of defense against the diverse pathogens we encounter in our lives. While the interactions between a single antibody and a single virus are routinely characterized in exquisite detail, the inherent tradeoffs between attributes such as potency and breadth remain unclear. In addition, there is a wide gap between the discrete interactions of single antibodies and how antibody mixtures collectively repel multiple viruses. Here, we develop a new form of antigenic cartography called a Neutralization Landscape that enumerates the full space of antibody-virus interactions for antibodies targeting the influenza hemagglutinin stem. This reference set of antibody behaviors transforms the potency-breadth tradeoff into a readily solvable geometry problem. Using the Neutralization Landscape, we decompose the collective neutralization from multiple antibodies to characterize the composition and functional properties of the stem antibodies within. Looking forward, this framework can leverage the serological assays routinely performed for influenza surveillance to analyze how an individual’s antibody repertoire evolves over time in response to vaccination or infection.

One-Sentence Summary

We describe the full range of behaviors for antibodies targeting the stem of influenza hemagglutinin, enabling us to decompose the collective behavior of antibody mixtures and characterize the individual antibodies within.
metabaR : an R package for the evaluation and improvement of DNA metabarcoding data quality
Authors: Zinger Lucie , Lionnet Clément , Benoiston Anne-Sophie , Donald Julian , Mercier Céline , Boyer Frédéric
Published: August 2020

DNA metabarcoding is becoming the tool of choice for biodiversity studies across taxa and large-scale environmental gradients. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines removing experimental noise have been designed to address this issue. However, these often only partially target produced artefacts, or are marker specific. In addition, assessments of data curation quality and the appropriateness of filtering thresholds are seldom available in existing pipelines, partly due to the lack of appropriate visualisation tools.

Here, we presentmetabaR, an R package that provides a comprehensive suite of tools to effectively curate DNA metabarcoding data after basic bioinformatic analyses. In particular,metabaRuses experimental negative or positive controls to identify different types of artefactual sequences, i.e. reagent contaminants and tag-jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those are available. Finally,metabaRprovides tools to visualise DNA metabarcoding data characteristics in their experimental context as well as their distribution, and facilitate assessment of the appropriateness of data curation filtering thresholds.

metabaRis applicable to any DNA metabarcoding experimental design but is most powerful when the design includes experimental controls and replicates. More generally, the simplicity and flexibility of the package makes it applicable any DNA marker, and data generated with any sequencing platform, and pre-analysed with any bioinformatic pipeline. Its outputs are easily usable for downstream analyses with any ecological R package.

metabaRcomplements existing bioinformatics pipelines by providing scientists with a variety of functions with customisable methods that will allow the user to effectively clean DNA metabarcoding data and avoid serious misinterpretations. It thus offers a promising platform for automatised data quality assessments of DNA metabarcoding data for environmental research and biomonitoring.
Aberrant RNA methylation triggers recruitment of an alkylation repair complex
Authors: Brickner Joshua R. , Tsao Ning , Rodell Rebecca , Oyeniran Clement , Lukinović Valentina , Bacolla Albino , Zhang Lisheng , Soll Jennifer M. , Casanova Alexandre G. , Ganguly Adit , He Chuan , Tainer John A. , Reynoird Nicolas , Mosammaparast Nima
Published: August 2020

A critical question in genome stability is the nature of the chemical damage responsible for repair activation. We previously reported a novel pathway specifically activated during alkylation damage in human cells, where the E3 ubiquitin ligase RNF113A mediates the recruitment of the ASCC repair complex. Yet the mechanistic basis for the alkylation damage selectivity of this pathway remains unclear. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. This aberrant RNA methylation causes transcriptional repression in a manner dependent on the ASCC complex. We show that an alkylated pre-mRNA, or an RNA containing a single damaged base, is sufficient to activate RNF113A E3 activity in a phosphorylation-dependent manner. Together, our work identifies an unexpected role for RNA damage in eliciting a DNA repair response, and suggests that RNA may serve as the “canary in the coal mine” for sensing alkylation damage.
Organisation of afferents along the anterior-posterior and medial-lateral axes of the rat orbitofrontal cortex
Authors: Barreiros Ines V. , Panayi Marios C. , Walton Mark E.
Published: August 2020

The orbitofrontal cortex (OFC) has been anatomically divided into a number of subregions along its medial-lateral axis, which behavioural research suggests have distinct functions. Recently, evidence has emerged suggesting functional diversity is also present along the anterior-posterior axis of the rodent OFC. However, the patterns of anatomical connections that underlie these differences have not been well characterised. Here, we use the retrograde tracer cholera toxin subunit B to simultaneously label the projections into the anterior lateral (ALO), posterior lateral (PLO), and posterior ventral (PVO) portions of the rat OFC. Our methodological approach allowed us to simultaneously compare the density and input patterns into these OFC subdivisions. We observed distinct and topographically organised projection patterns into ALO, PLO, and PVO from the mediodorsal and the submedius nuclei of the thalamus. We also observed different levels of connectivity strength into these OFC subdivisions from the amygdala, motor cortex, sensory cortices and medial prefrontal cortical structures, including medial OFC, infralimbic and prelimbic cortices. Interestingly, while labelling in some of these input regions revealed only a gradient in connectivity strength, other regions seem to project almost exclusively to specific OFC subdivisions. Moreover, differences in input patterns between ALO and PLO were as pronounced as those between PLO and PVO. Together, our results support the existence of distinct anatomical circuits within lateral OFC along its anterior-posterior axis.
Color morphs of the coral,Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes
Authors: Satoh Noriyuki , Kinjo Koji , Shintaku Kohei , Kezuka Daisuke , Ishimori Hiroo , Yokokura Atsushi , Hagiwara Kazutaka , Hisata Kanako , Kawamitsu Mayumi , Koizumi Koji , Shinzato Chuya , Zayasu Yuna
Published: August 2020

Corals of the family Acroporidae are key structural components of reefs that support the most diverse marine ecosystems. Due to increasing anthropogenic stresses, coral reefs are in decline. Along the coast of Okinawa, Japan, three different color morphs ofAcropora tenuishave been recognized for decades. These include brown (N morph), yellow-green (G) and purple (P) forms. The tips of axial coral polyps exhibit specific fluorescence spectra. This attribute is inherited asexually, and color morphs do not change seasonally. In Okinawa Prefecture, during the summer of 2017, the N and P morphs experienced bleaching, in which some N morphs died while P morphs recovered. In contrast, G morphs successfully withstood the stress. Symbiotic dinoflagellates are essential symbiotic partners of scleractinian corals. Photosynthetic activity of symbionts was reduced in July in N and P morphs; however, the three color-morphs host similar sets of Clade-C zoothanthellae, suggesting that beaching of N and P morphs cannot be attributed to differences in symbiont clades. The decodedAcropora tenuisgenome includes five genes for green fluorescent proteins (GFP), two for cyan fluorescent proteins (CFP), three for red fluorescent proteins (RFP), and seven genes for chromoprotein (ChrP). A summer survey of gene expression profiles demonstrated that (a) expression of CFP and REP was quite low in all three morphs, (b) P morphs expressed higher levels of ChrP, (c) both N and G morphs expressed GFP highly, and (d) GFP expression was reduced in N morphs, compared to G morphs, which maintained higher levels of GFP expression throughout the summer. Although further studies are required to understand the biological significance of these color morphs ofAcropora tenuis, our results suggest that thermal stress resistance is modified by genetic mechanisms that coincidentally lead to diversification of color morphs.
Nuclear stiffness decreases with disruption of the extracellular matrix in living tissues
Authors: McCreery Kaitlin P. , Xu Xin , Scott Adrienne K. , Fajrial Apresio K. , Calve Sarah , Ding Xiaoyun , Neu Corey P.
Published: August 2020

Reciprocal interactions between the cell nucleus and the extracellular matrix lead to macroscale tissue phenotype changes. The extracellular environment is physically linked to the nuclear envelope and provides cues to maintain nuclear structure and cellular homeostasis regulated in part by mechanotransduction mechanisms. However, little is known about how structure and properties of the extracellular matrix in living tissues impacts nuclear mechanics, and current experimental challenges limit the ability to detect and directly measure nuclear mechanics while cells are within the native tissue environment. Here, we hypothesized that enzymatic disruption of the tissue matrix results in a softer tissue, affecting the stiffness of embedded cell and nuclear structures. We aimed to directly measure nuclear mechanics without perturbing the native tissue structure to better understand nuclear interplay with the cell and tissue microenvironments. To accomplish this, we expanded an atomic force microscopy needle-tip probe technique that probes nuclear stiffness in cultured cells to measure the nuclear envelope and cell membrane stiffness within native tissue. We validated this technique by imaging needle penetration and subsequent repair of the plasma and nuclear membranes of HeLa cells stably expressing the membrane repair protein CHMP4B-GFP. In the native tissue environmentex vivo, we found that while enzymatic degradation of viable cartilage tissues with collagenase 3 (MMP-13) and aggrecanase-1 (ADAMTS-4) decreased tissue matrix stiffness, cell and nuclear membrane stiffness is also decreased. Finally, we demonstrated the capability for cell and nucleus elastography using the AFM needle-tip technique. These results demonstrate disruption of the native tissue environment that propagates to the plasma membrane and interior nuclear envelope structures of viable cells.
Epigenetic regulation of differentially expressed genes between various glioma types
Authors: Grabowicz Ilona E. , Wilczyński Bartek , Kamińska Bożena , Roura Adria-Jaume , Wojtaś Bartosz , Dąbrowski Michał J.
Published: August 2020

Gliomas are the most frequent primary tumors of the central nervous system (CNS) and encompass two major subgroups: diffuse, malignant gliomas and benign, well differentiated gliomas showing a more circumscribed growth. Genome-wide next generation sequencing studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different types of gliomas improving tumor diagnosis and having important implications for future clinical trials and patient management. We have recently created a unique resource encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we took advantage of a wealth of data from those high-throughput experiments, intersected those data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found a set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing glioma-related genes. Moreover, many genes associated with the cell-matrix adhesion Gene Ontology group, in particular 14PROTOCADHERINs, were found to be regulated by the long range contacts with enhancers. Overall, the results presented here demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy. We demonstrated that integration of whole genome epigenetic data with Hi-C data and transcriptomic profiles described in this work, can segregate low and high grade gliomas and reveal new regulatory networks that could explain some of the functional differences between gliomas of different malignancies.

Highlights

Integration of ATAC-seq, ChIP-seq and RNA-seq reveals glioma malignancy-related gene regulatory networks.

TADs segmentation contributes to gene-epigenetically modified enhancer relationships.

Contacts of active enhancers in gliomas of different malignancies might affect expression of genes involved in cancerogenesis, such asPROTOCADHERINsorEGFR.
Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage
Authors: Liu Jonathan , Hansen Donald , Eck Elizabeth , Kim Yang Joon , Turner Meghan , Alamos Simon , Garcia Hernan G.
Published: August 2020

The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, theirin vivodissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
Expansion Revealing: Decrowding Proteins to Unmask Invisible Brain Nanostructures
Authors: Sarkar Deblina , Kang Jinyoung , Wassie Asmamaw T , Schroeder Margaret E. , Peng Zhuyu , Tarr Tyler B. , Tang Ai-Hui , Niederst Emily , Young Jennie. Z. , Tsai Li-Huei , Blanpied Thomas A. , Boyden Edward S.
Published: August 2020

Cells and tissues are made out of nanoscale building blocks, such as proteins, organized in crowded nanostructures. We show that many biomolecules, and the nanostructures in which they are embedded, may be invisible to prior imaging techniques, due to the inaccessibility of labels (e.g., antibodies) to biomolecules embedded within such crowded structures. We developed a technology, expansion revealing (ExR), which isotropically decrowds proteins from each other, to enable their labeling. We use ExR to discover the alignment of presynaptic calcium channels with postsynaptic machinery in intact brain circuits, as well as the existence of periodic amyloid nanoclusters containing ion channel proteins in Alzheimer’s model mice. Thus, ExR reveals nanostructures within complex biological specimens that were not previously visualizable, and may find broad use in biology.

One Sentence Summary

De-crowding biomolecules with Expansion Revealing unmasks fundamentally new nanostructures in intact brain tissue, which remained invisible otherwise.
Lattice micropatterning for cryo-electron tomography studies of cell-cell contacts
Authors: Engel Leeya , Vasquez Claudia G. , Montabana Elizabeth A. , Sow Belle M. , Walkiewicz Marcin P. , Weis William I. , Dunn Alexander R.
Published: August 2020

Cryo-electron tomography is the highest resolution tool available for structural analysis of macromolecular complexes within their native cellular environment. At present, data acquisition suffers from low throughput, in part due to the low probability of positioning a cell such that the subcellular structure of interest is on a region of the electron microscopy (EM) grid that is suitable for imaging. Here, we photo-micropatterned EM grids to optimally position endothelial cells so as to enable high-throughput imaging of cell-cell contacts. Lattice micropatterned grids increased the average distance between intercellular contacts and the thicker cell nuclei such that the regions of interest were sufficiently thin for direct imaging. We observed a diverse array of membranous and cytoskeletal structures at intercellular contacts, demonstrating the utility of this technique in enhancing the rate of data acquisition for cellular cryo-electron tomography studies.
The subcellular architecture of thexylgene expression flow of the TOL catabolic plasmid ofPseudomonas putidamt-2
Authors: Kim Juhyun , Goñi-Moreno Angel , de Lorenzo Víctor
Published: August 2020

Despite intensive research on the biochemical and regulatory features of the archetypal catabolic TOL system borne by pWW0 ofPseudomonas putidamt-2, the physical arrangement and tridimensional logic of thexylgene expression flow remains unknown. In this work, the spatial distribution of specificxylmRNAs with respect to the host nucleoid, the TOL plasmid and the ribosomal pool has been investigated.In situhybridization of target transcripts with fluorescent oligonucleotide probes revealed thatxylmRNAs cluster in discrete foci, adjacent but clearly separated from the TOL plasmid and the cell nucleoid. Also, they co-localize with ribosome-rich domains of the intracellular milieu. This arrangement was kept even when thexylgenes were artificially relocated at different chromosomal locations. The same happened when genes were expressed through a heterologous T7 polymerase-based system, which originated mRNA foci outside the DNA. In contrast, rifampicin treatment, known to ease crowding, blurred the confinement ofxyltranscripts. This suggested thatxylmRNAs intrinsically run away from their initiation sites to ribosome-rich points for translation—rather than being translated coupled to transcription. Moreover, the results suggest that the distinct subcellular motion ofxylmRNAs results both from innate properties of the sequence at stake and the physical forces that keep the ribosomal pool away from the nucleoid inP. putida. This scenario is discussed on the background of current knowledge on the 3D organization of the gene expression flow in other bacteria and the environmental lifestyle of this soil microorganism.

IMPORTANCE

The transfer of information between DNA, RNA and proteins in a bacterium is often compared to the decoding of a piece of software in a computer. However, the tridimensional layout and the relational logic of the cognate biological hardware i.e. the nucleoid, the RNA polymerase and the ribosomes, are habitually taken for granted. In this work we inspected the localization and fate of the transcripts that stem from the archetypal biodegradative plasmid pWW0 of soil bacteriumPseudomonas putidaKT2440 through the non-homogenous milieu of the bacterial cytoplasm. The results expose that— similarly to computers also—the material components that enable the expression flow are well separated physically and they decipher the sequences through a distinct tridimensional arrangement with no indication of transcription/translation coupling. We argue that the resulting subcellular architecture enters an extra regulatory layer that obeys a species-specific positional code that accompanies the environmental lifestyle of this bacterium.
Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization
Authors: Bashkirova Elizaveta , Monahan Kevin , Campbell Christine E. , Osinski Jason M. , Tan Longzhi , Schieren Ira , Barnea Gilad , Xie X. Sunnie , Gronostajski Richard M. , Lomvardas Stavros
Published: August 2020

Expression of one out of >1000 olfactory receptor (OR) genes is stochastic but, yet, spatially organized in stereotypic anatomical segments, or “zones”, along the dorsoventral axis of the mouse olfactory epithelium. We discovered that zonal OR expression is specified by OR chromatin structure and genome architecture during olfactory neuron differentiation. Specifically, across every zone dorsally expressed ORs have higher levels of heterochromatic marks and long-range contacts than ORs expressed ventrally. However, OR heterochromatin levels and frequency of genomic contacts between ORs gradually increase towards ventral zones. Consequently, ORs from dorsal indexes accumulate high H3K9me3/H3K79me3 enrichment and become silenced in ventral zones, while ORs from ventral indexes lack activating long-range genomic interactions and, thus, cannot be chosen in dorsal segments. This process is regulated by NFIA, B, and X gradients along the dorsoventral axis, triple deletion of which causes homeotic transformations on zonal OR expression, heterochromatin formation, and genomic compartmentalization.