bluuebunny/crossref_metadata_2025 huggingface dataset:
The American College of Rheumatology Fibromyalgia Criteria Are Useful in the Evaluation of Fibromyalgia Symptoms in Patients With Ankylosing Spondylitis
Authors: Magrey Marina N. , Thomas Charles , Khan Muhammad Asim
Published: July 2020

Background

Fibromyalgia (FM) is common among patients with ankylosing spondylitis (AS), and its coexistence is believed to interfere with the measurement of patient-reported outcomes of disease activity and function in AS because of overlapping symptoms between the 2 diseases. This can confound clinical assessment and treatment decisions.

Aims

The aim of this study was to assess the relationship between the Fibromyalgia Symptom Scale (FSS) and its components, the Widespread Pain Index (WPI), and System Severity Scale with measures of disease activity, function, and patient-reported outcomes in AS.

Methods

We recruited 63 AS patients (aged ≥18 years) meeting the modified New York criteria, and Bath Ankylosing Spondylitis Disease Activity Index, Ankylosing Spondylitis Disease Activity Score–C-Reactive Protein, Routine Assessment of Patient Index Data 3, and Bath Ankylosing Spondylitis Functional Index questionnaires were administered to them. The presence of FM was determined using validated 2010 American College of Rheumatology diagnostic criteria for FM.

Results

Twenty-eight of 63 patients (44.4%) with AS and FM had higher disease activity and greater impairment of functional ability compared with AS patients without FM. Using multiple linear regression estimates, there was no significant relationship of FSS scores with Bath Ankylosing Spondylitis Disease Activity Index (p = 0.36), Routine Assessment of Patient Index Data 3 (p = 0.50), Ankylosing Spondylitis Disease Activity Score–C-Reactive Protein (p = 0.24), Bath Ankylosing Spondylitis Functional Index (p = 0.42) scores, or erythrocyte sedimentation rate (p = 0.82) and C-reactive protein (p = 0.75).

Conclusions

Despite a high prevalence of FM in our patients with the diagnosis of AS, there was no relationship between FSS and measures of disease activity or function in AS, suggesting that FSS and its components could be a useful tool to assess FM in AS patients. Also, FM impairs functional ability in patients with AS.
A Case of Myotonic Dystrophy Type I With Rimmed Vacuoles in Skeletal Muscle Pathology
Authors: Ban Rui , Zhang Yutong , Li Ke , Shi Qiang
Published: July 2020

Dystrophia myotonica type 1 (DM1) and DM2 are the most common muscular dystrophies. In both diseases, the skeletal muscle is the most severely affected. Additional symptoms are also involved in the eye, heart, brain, endocrine glands, gastrointestinal tract, skin, skeleton, and peripheral nerves. Skeletal muscle pathology is mainly manifested as myopathic changes including internal nuclei, sarcoplasmic masses, preferential type 1 fiber atrophy, and so on. Rimmed vacuoles (RVs) seen on muscle biopsy are areas of muscle destruction with an accumulation of autophagic vacuoles. However, there is no report about RVs in skeletal muscle of myotonic dystrophy patients. Here, we describe the first case of DM1 with RVs in skeletal muscle pathology.
Progression of Large Vessel Disease in Patients With Giant Cell Arteritis–Associated Ischemic Stroke: The Role of Vascular Imaging
Authors: Guisado-Alonso Daniel , Edo M. Carmen , Estrada Alarcón Paula Valentina , García-Sánchez Sonia María , Font Maria Àngels , Mena Romo Luis , Marrero-González Paula , Mengual Juan José , Castrillo Laura , Montull Caterina , Corominas Hector , Gómez-Choco Manuel
Published: July 2020

Objective

Giant cell arteritis (GCA) can cause ischemic stroke (IS) due to the involvement of the internal carotid and vertebral arteries. The aim of our study is to describe the pattern of stroke recurrence in patients with GCA-related IS and the role of vascular imaging in the follow-up of these patients.

Methods

We conducted an observational study of 2417 consecutive patients diagnosed with IS and admitted to our hospital from January 2012 to December 2018. We reviewed patients with GCA-related IS and the relationship of erythrocyte sedimentation rate, C-reactive protein, vascular status, and clinical course.

Results

We found 4 patients with GCA-related IS among 2417 IS patients: 1 woman (25%); median age, 77.3 years (67–85 years). Mean follow-up was 3.6 years. Initial vascular workup showed vertebral artery stenosis in all of them and internal carotid artery stenosis in 2 patients. All patients were started on treatment with full-dose prednisone, associated with methotrexate in 2 cases. Follow-up color-coded duplex sonography disclosed progression of arterial stenoses in 3 patients who suffered a recurrent IS (days after index stroke; mean, 27.67 [SD, 10.97]) despite normal C-reactive protein and erythrocyte sedimentation rate values.

Conclusions

Vascular imaging, especially with color-coded duplex sonography, could play a role in the follow-up of patients with GCA-related IS and identify those patients with higher risk of recurrent stroke.
Guidelines for the Responsible Use of Deception in Simulation
Authors: Calhoun Aaron W. , Pian-Smith May , Shah Anjan , Levine Adam , Gaba David , DeMaria Samuel , Goldberg Andrew , Meyer Elaine C.
Published: July 2020

Summary Statement

Many techniques and modifications commonly used by the simulation community have been identified as deceptive. Deception is an important issue addressed by both the newly adopted Healthcare Simulationist Code of Ethics and the American Psychological Association Code of Conduct. Some view these approaches as essential whereas others question their necessity as well as their untoward psychological effects. In an attempt to offer guidance to simulation-based healthcare educators, we explore educational practices commonly identified as deceptive along with their potential benefits and detriments. We then address important decision points and high-risk situations that should be avoided to uphold ethical boundaries and psychological safety among learners. These are subsequently analyzed in light of the Code of Ethics and used to formulate guidelines for educators that are intended to ensure that deception, when necessary, is implemented in as psychologically safe a manner as possible.
Effects of Team Size and a Decision Support Tool on Healthcare Providers' Workloads in Simulated Neonatal Resuscitation
Authors: Roitsch Charles M. , Hagan Joseph L. , Patricia Karen E. , Jain Seema , Chen Xinpu , Arnold Jennifer L. , Devaraj Sridevi , Sundgren Nathan C.
Published: July 2020

Introduction

Optimal resuscitation team size for workload distribution among team members is not known. In addition, decision support tools (DSTs) are available to improve team performance, but the effect on workload is not known. Because increased workload can impair performance, we aimed to determine whether team size or use of a DST alters workload in healthcare providers (HCPs) while performing neonatal resuscitation.

Methods

We report a substudy of a randomized, 2 × 2 factorial design study using 109 Neonatal Resuscitation Program–trained HCPs. Healthcare providers were randomized to 1 of 4 permutations, including team size of 2 versus 3 and using DST versus memory alone while performing 2 simulated neonatal resuscitations. The HCPs' workload was assessed by the National Aeronautics and Space Administration Task Load Index obtained after each scenario. Mixed effects linear models compared the effect of team size and DST use on National Aeronautics and Space Administration Task Load Index scores.

Results

When all team members were combined, there was an increased workload in teams of 2 HCPs compared with teams of 3 and was primarily due to an increase in workload on the team leaders. Decision support tool use increased workload for the other team members in the first of the 2 scenarios but did not increase workload in the second scenario.

Conclusions

Teams of 2 HCPs reported a higher workload compared with teams of 3 HCPs. Decision support tool use can increase workload for other team members when first introduced as a new task. This study highlights the need to consider factors that negatively affect mental workload when determining the composition of a resuscitation team.
Supportive and palliative care for people with respiratory problems and preexisting serious mental illness
Authors: Peryer Guy , Barnes Sylvia , Farquhar Morag
Published: July 2020

Purpose of review

People living with serious mental illness are at a higher risk of developing respiratory problems that can lead to increased morbidity and early mortality. This review aimed to identify recent advances in care provision for people with respiratory problems and preexisting serious mental illness to ease symptom burden and reduce the risk of premature mortality.

Recent findings

Intervention-based studies in this area are scarce. The evidence reviewed originated from observational studies. Concluding comments from the synthesis suggest there are specific needs for proactive screening of respiratory function as part of routine physical health checks across care settings for people living with serious mental illness, more stringent monitoring of comorbid chronic lung conditions and increased attention in reducing the frequency respiratory infections. Integrated services across care settings are needed to support people with serious mental illness to limit the impact of modifiable lifestyle factors known to be detrimental to respiratory health, such as smoking.

Key priorities are identified to improve accessibility and inclusivity of respiratory care pathways for people living with serious mental illness to support early detection and proactive monitoring of respiratory problems to help reduce the risk of early mortality.
Schizophrenia and cancer
Authors: González-Rodríguez Alexandre , Labad Javier , Seeman Mary V.
Published: July 2020

Purpose of review

The cancer mortality rate in persons with schizophrenia is higher than it is in the general population. The purpose of this review is to determine why, and to identify solutions.

Recent findings

The recent literature points to three groups of reasons why mortality is high: patient reasons such as nonadherence to treatment, provider reasons such as diagnostic overshadowing, and health system reasons such as a relative lack of collaboration between medicine and psychiatry. Strategies for cancer prevention, early detection, and effective treatment are available but difficult to put into practice because of significant barriers to change, namely poverty, cognitive and volitional deficits, heightened stress, stigma, and side effects of antipsychotic medication. The literature makes recommendations about surmounting these barriers and also offers suggestions with respect to support and palliative care in advanced stages of cancer. Importantly, it offers examples of effective collaboration between mental health and cancer care specialists.

The high mortality rate from cancer in the schizophrenia population is a matter of urgent concern. Although reasons are identifiable, solutions remain difficult to implement. As we work toward solutions, quality palliative care at the end of life is required for patients with severe mental illness.

Video abstract

http://links.lww.com/COSPC/A24
Regional Performance of Apical Support Procedures at Time of Hysterectomy for Benign Indications: What Is the Role of Surgeon Training?
Authors: Putman Jessica G. , Meister Melanie R. , Lenger Stacy M. , Lowder Jerry L.
Published: July 2020

Objective

The objective of this study was to determine factors associated with performance of concomitant apical support procedures (ASPs) with benign hysterectomy at a regional medical system.

Methods

Benign hysterectomies performed within 1 regional medical system from January 2011 to November 2017 were identified using International Classification of Diseases, Ninth and 10th Revision, and Current Procedural Terminology codes. Primary outcome was performance of concomitant ASP. χ2 Tests compared categorical variables. Multivariable logistic regression analysis was performed to determine factors associated with performance of concomitant ASP.

Results

A total of 12,345 benign hysterectomies were performed during the study period. Uterovaginal prolapse was the primary diagnosis in 924 (7.48%) hysterectomies and an associated diagnosis in 1180 (9.56%) hysterectomies. A total of 686 patients (5.56%) had concurrent ASPs: 119 (17.3%) in patients without a diagnosis of prolapse and 567 (82.7%) with prolapse. Using multivariable logistic regression, controlling for age, race, insurance type, hospital type, procedure year, hysterectomy route, and surgeon training in patients with a diagnosis of prolapse, older age, supracervical hysterectomy, and surgeon training were associated with performance of ASPs.

Conclusions

Even in patients with a preoperative diagnosis of uterovaginal prolapse, ASPs are not routinely performed at time of hysterectomy. Fellowship-trained surgeons were more likely to perform ASPs. Ongoing educational efforts during training and postgraduate at the national and regional level on the importance of reestablishing apical vaginal support at time of hysterectomy is needed to prevent incident and recurrent post-hysterectomy vaginal vault prolapse.
Six novel species of the obligate marine actinobacterium Salinispora, Salinispora cortesiana sp. nov., Salinispora fenicalii sp. nov., Salinispora goodfellowii sp. nov., Salinispora mooreana sp. nov., Salinispora oceanensis sp. nov. and Salinispora vitiensis sp. nov., and emended description of the genus Salinispora
Authors: Román-Ponce Brenda , Millán-Aguiñaga Natalie , Guillen-Matus Dulce , Chase Alexander B. , Ginigini Joape G.M. , Soapi Katy , Feussner Klaus D. , Jensen Paul R. , Trujillo Martha E.
Published: July 2020

Ten representative actinobacterial strains isolated from marine sediments collected worldwide were studied to determine their taxonomic status. The strains were previously identified as members of the genus

Salinispora

and shared >99 % 16S rRNA gene sequence similarity to the three currently recognized

Salinispora

species. Comparative genomic analyses resulted in the delineation of six new species based on average
nucleotide identity and digital DNA–DNA
hybridization values below 95 and 70 %, respectively. The species status of the six new groups was supported by a core-genome phylogeny reconstructed from 2106 orthologs detected in 118 publicly available

Salinispora

genomes. Chemotaxonomic and physiological studies were used to complete the phenotypic characterization of the strains. The fatty acid profiles contained the major components iso-C16 : 0, C15 : 0, iso-17 : 0 and anteiso C17 : 0. Galactose and xylose were common in all whole-sugar patterns but differences were found between the six groups of strains. Polar lipid compositions were also unique for each species. Distinguishable physiological and biochemical characteristics were also recorded. The names proposed are Salinispora cortesiana sp. nov., CNY-202T (=DSM 108615T=CECT 9739T); Salinispora fenicalii sp. nov., CNT-569T (=DSM 108614T=CECT 9740T); Salinispora goodfellowii sp. nov., CNY-666T (=DSM 108616T=CECT 9738T); Salinispora mooreana sp. nov., CNT-150T (=DSM 45549T=CECT 9741T); Salinispora oceanensis sp. nov., CNT-138T (=DSM 45547T=CECT 9742T); and Salinispora vitiensis sp. nov., CNT-148T (=DSM 45548T=CECT 9743T).
List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
Authors: Parte Aidan C. , Sardà Carbasse Joaquim , Meier-Kolthoff Jan P. , Reimer Lorenz C. , Göker Markus
Published: July 2020

The List of Prokaryotic names with Standing in Nomenclature (LPSN) was acquired in November 2019 by the DSMZ and was relaunched using an entirely new production system in February 2020. This article describes in detail the structure of the new site, navigation, page layout, search facilities and new features.
Sandaracinobacter neustonicus sp. nov., isolated from the sea surface microlayer in the Southwestern Pacific Ocean, and emended description of the genus Sandaracinobacter
Authors: Lee Inae , Jang Gwang Il , Cho Yirang , Yoon Soo Jung , Pham Ha My , Nguyen Anh Vu , Lee Yung Mi , Park Hyun , Rhee Tae Siek , Kim Sae Hun , Hwang Chung Yeon
Published: July 2020

A Gram-stain-negative, non-motile, facultatively anaerobic and rod-shaped bacterial strain, designated PAMC 28131T, was isolated from a sea surface microlayer sample in the open water of the Pacific Ocean. Phylogenetic analysis of the 16S rRNA gene sequence of strain PAMC 28131Trevealed an affiliation to the genusSandaracinobacterwith the closest speciesSandaracinobacter sibiricusRB16-17T(sequence similarity of 98.2 %). Strain PAMC 28131Twas able to grow optimally with 0.5–1.0 % NaCl and at pH 6.5–7.0 and 30 °C. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The major cellular fatty acids (>10 %) were C18 : 1 ω6cand/or C18 : 1 ω7c,(42.6 %), C17 : 1 ω6c(19.3 %) and C16 : 1 ω6cand/or C16 : 1 ω7c(15.8 %), and the respiratory quinone was Q-10. The genomic DNA G+C content was 65.3 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain PAMC 28131Tcould be clearly distinguished fromS. sibiricusRB16-17T. Thus, strain PAMC 28131Tshould be classified as representing a novel species in the genusSandaracinobacter, for which the nameSandaracinobacter neustonicussp. nov. is proposed. The type strain is PAMC 28131T(=KCCM 43127T=JCM 30734T).
Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521T as Actinomadura lepetitiana sp. nov.
Authors: Dalmastri Claudia , Gastaldo Luciano , Berini Francesca , Marinelli Flavia , Marcone Giorgia Letizia
Published: July 2020

The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus

Actinomadura

on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus Actinomadura, and it was most closely related to

Actinomadura bangladeshensis

DSM 45347T (99.31 % similarity) and

Actinomadura mexicana

DSM 44485T (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained meso-2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H6), with minor amounts of MK-9(H8) and MK-9(H4). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C16 : 0 and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of C18:1ω9c, C16:1ω7c and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA–DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus

Actinomadura

, for which the name Actinomadura lepetitiana sp. nov. is proposed. The type strain is NRRL B-65521T(=LMG 31258T=DSM 109019T).
Chitinophaga solisilvae sp. nov., isolated from forest soil
Authors: Ping Weiwei , Zhang Ying , Pang Huancheng , Zhang Jun , Li Dai , Li Yuyi , Zhang Jianli
Published: July 2020

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, O9T, was isolated from a forest soil sample collected at Dai, Xishuangbanna, Yunnan Province, PR China. Strain O9T grew optimally at pH 7.0, at 28‒30 °C and in the absence of NaCl. 16S rRNA gene sequence analysis placed strain O9T within the genus

Chitinophaga

of the family Chitinophagaceae, with

Chitinophaga terrae

KP01T (97.8 %),

Chitinophaga jiangningensis

JN53T (97.7 %),

Chitinophaga niastensis

JS16-4T (97.4 %),

Chitinophaga qingshengii

JN246T (97.3 %) and

Chitinophaga dinghuensis

DHOC24T (97.3 %) as its closest relatives. Strain O9T hydrolysed casein, gelatin and Tween 80. It could not assimilate l-arabinose, l-rhamnose, sucrose, melibiose, gentiobiose or d-fructose as a carbon source. It was negative for esterase lipase (C8) and β-glucosidase. Phosphatidylethanolamine was the predominant polar lipid. The major respiratory quinone of strain O9T was MK-7. Its major fatty acids were iso-C15:0 (34.2 %), C16:1
ω5c (20.9 %) and iso-C17:0 3-OH (12.6 %). The genomic DNA G+C content of strain O9T was 49.0 mol% based on total genome calculations. The average nucleotide identity score between the genomic sequence of strain O9T and that of

Chitinophaga terrae

KP01T was 72.9%. The Genome-to-Genome Distance Calculator showed that DNA‒DNA hybridization values for strain O9T and

Chitinophaga terrae

KP01T were 13.6, 21.1 and 14.4%, respectively. Based on the polyphasic taxonomic data, strain O9T represents a novel species of the genus

Chitinophaga

, for which the name Chitinophaga solisilvae sp. nov. is proposed. The type strain is O9T (=CGMCC 1.12462T=KCTC 32404T).
Managing the risk of a COVID-19 outbreak from border arrivals
Authors: Steyn Nicholas , Plank Michael J. , James Alex , Binny Rachelle N. , Hendy Shaun C. , Lustig Audrey
Published: July 2020

In an attempt to maintain elimination of COVID-19 in New Zealand, all international arrivals are required to spend 14 days in government-managed quarantine and to return a negative test result before being released. We model the testing, isolation and transmission of COVID-19 within quarantine facilities to estimate the risk of community outbreaks being seeded at the border. We use a simple branching process model for COVID-19 transmission that includes a time-dependent probability of a false negative test result. We show that the combination of 14-day quarantine with two tests reduces the risk of releasing an infectious case to around 0.1% per infected arrival. Shorter quarantine periods, or reliance on testing only with no quarantine, substantially increases this risk. We calculate the fraction of cases detected in the second week of their two week stay and show that this may be a useful indicator of the likelihood of transmission occurring within quarantine facilities. Frontline staff working at the border risk exposure to infected individuals and this has the potential to lead to a community outbreak. We use the model to test surveillance strategies and evaluate the likely size of the outbreak at the time it is first detected. We conclude with some recommendations for managing the risk of potential future outbreaks originating from the border.
SECOND WEEK METHYL-PREDNISOLONE PULSES IMPROVE PROGNOSIS IN PATIENTS WITH SEVERE CORONAVIRUS DISEASE 2019 PNEUMONIA: AN OBSERVATIONAL COMPARATIVE STUDY USING ROUTINE CARE DATA
Authors: Ruiz-Irastorza Guillermo , Pijoan Jose-Ignacio , Bereciartua Elena , Dunder Susanna , Dominguez Jokin , Garcia-Escudero Paula , Rodrigo Alejandro , Gomez-Carballo Carlota , Varona Jimena , Guio Laura , Ibarrola Marta , Ugarte Amaia , Martinez-Berriotxoa Agustin
Published: July 2020

OBJECTIVE

To analyze the effects of a short course of methyl-prednisolone pulses (MP) during the second week of disease (week-2) in patients with severe coronavirus disease 2019 (COVID-19) pneumonia.

METHODS

Comparative observational study using data collected from routine care at Hospital Universitario Cruces, Barakaldo, Bizkaia, Spain in patients with COVID-19 pneumonia. We compared patients who received week-2-MP (125250 mg/d x3) with those who did not, with the end-points time to death and time to death or endotracheal intubation.

RESULTS

We included 242 patients with COVID-19 pneumonia and elevated inflammatory markers at admission. Sixty-one patients (25%) received week-2-MP. Twenty-two patients (9%) died and 31 (12.8%) suffered death or intubation. The adjusted HRs for death and death or intubation for patients in the week-2-MP group were 0.35 (95%CI 0.11 to 1.06, p= 0.064) and 0.33 (95%CI 0.13 to 0.84, p=0.020), respectively. These differences were specifically seen in the subcohort of patients with a SpO2/FiO2 at day 7 lower than 353 (adjusted HR 0.31, 95% CI 0.08 to 1.12, p=0.073 and HR 0.34, 95%CI 0.12 to 0.94, p=0.038, respectively) but not in patients with higher SpO2/FiO2. Patients receiving out-of-week-2-MP, non-pulse glucocorticoids or no glucocorticoids had an increased adjusted risk for both outcomes compared with week-2-MP group: HR 5.04 (95% CI 0.91-27.86), HR 10.09 (95% CI 2.14-47.50), HR 4.14 (95% CI 0.81-21.23), respectively, for death; HR 7.38 (95% CI 1.86-29.29), HR 13.71 (95% CI 3.76-50.07), HR 3.58 (95% CI 0.89-14.32), respectively, for death or intubation. These differences were significant only in the subgroup with low SpO2/FiO2.

CONCLUSIONS

Week-2-MP are effective in improving the prognosis of patients with COVID-19 pneumonia with features of inflammatory activity and respiratory deterioration entering the second week of disease. The recognition of this high-risk population should prompt early use of MP at this point.
A national consensus management pathway for Paediatric Inflammatory Multisystem Syndrome - Temporally associated with SARS-CoV-2 (PIMS-TS): The results of a national Delphi process
Authors: Harwood Rachel , Allin Benjamin , Jones Christine E , Whittaker Elizabeth , Ramnarayan Padmanabhan , Ramanan Athimalaipet , Kaleem Musa , Tulloh Robert , Peters Mark J , Almond Sarah , Davis Peter J , Levin Michael , Faust Saul N. , Knight Marian , Kenny Simon
Published: July 2020

Objective

To develop a consensus management pathway for children with Paediatric Inflammatory Multisystem Syndrome - Temporally associated with SARS-CoV-2 (PIMS-TS).

Design

A three-phase online Delphi process and virtual consensus meeting sought consensus over the investigation, management and research priorities from 98 multidisciplinary participants caring for children with PIMS-TS. 46 participants (47%) completed all three phases. Participants were grouped into three panels and scored each statement from 1 (disagree) to 9 (strongly agree). In phase two participants were shown their panel’s scores, and in phase three all panels’ scores.

Consensus agreement was defined as ≥70% of participants in each panel scoring the statement 7-9, and <15% scoring 1-3, and consensus disagreement was the opposite of this. Statements which achieved consensus in 2/3 panels were discussed at the consensus meeting, and when ≥70% participants agreed with the statement it achieved consensus.

Results

255 statements were assessed, with ‘consensus agreement’ achieved for 111 (44%), ‘consensus disagreement’ for 29 (11%), and no consensus for 115 (45%). The 140 consensus statements were used to derive the consensus management pathway.

Conclusions

A national consensus pathway has been developed for children suspected of having the novel syndrome PIMS-TS in a timely, cost-efficient manner, in the midst of a global pandemic. Use of a rapid online Delphi process has made this consensus process possible. Future evidence will inform updates to this guidance, which in the interim provides a solid framework to support clinicians caring for children with PIMS-TS.
Genomic adaptations to an endolithic lifestyle in the coral-associated algaOstreobium
Authors: Iha Cintia , Dougan Katherine E. , Varela Javier A. , Avila Viridiana , Jackson Christopher J. , Bogaert Kenny A. , Chen Yibi , Judd Louise M. , Wick Ryan , Holt Kathryn E. , Pasella Marisa M. , Ricci Francesco , Repetti Sonja I. , Medina Mónica , Marcelino Vanessa R. , Chan Cheong Xin , Verbruggen Heroen
Published: July 2020

The green algaOstreobiumis an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts.Ostreobiumlives in the coral’s skeleton, a low-light environment with variable pH and O□ availability. We present theOstreobiumnuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding ofOstreobium’s adaptations to its extreme environment and its roles as a coral holobiont member. TheOstreobiumgenome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests thatOstreobiummay supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allow it to live in the anoxic skeleton at night.Ostreobiumdepends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showedOstreobiumbecoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and differentOstreobiumgenotypes. Our work provides a comprehensive understanding of the adaptations ofOstreobiumto its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching and recovery.
Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA transcripts is driven by intron retention: implications for RNA-directed therapies
Authors: Dumbović Gabrijela , Braunschweig Ulrich , Langner Heera K. , Jastrzebska Katarzyna , Smallegan Michael , Blencowe Benjamin , Cech Thomas R. , Caruthers Marvin H. , Rinn John L.
Published: July 2020

Numerous global connections have been made between splicing and other layers of gene regulation, including the spatial partitioning of the transcriptome in the cell. Yet, there has been surprisingly little analysis of the spatio-temporal regulation of individual protein-coding and non-coding RNA molecules in single cells. Here we address how intron retention influences the spatio-temporal dynamics of transcripts from two clinically relevant genes: TERT (Telomerase Reverse Transcriptase) pre-mRNA and TUG1 (Taurine-Upregulated Gene 1) lncRNA. Single molecule RNA FISH revealed that nuclear TERT transcripts uniformly and robustly retain two specific introns whose splicing occurs during mitosis. In contrast, TUG1 has a bimodal distribution of fully spliced cytoplasmic and intron-retained nuclear transcripts. We further test the functionality of intron-retention events using RNA-targeting thiomorpholino antisense oligonucleotides to block intron excision. We show that intron retention is the driving force for the nuclear compartmentalization of these RNAs. For both RNAs, altering this splicing-driven subcellular distribution had significant effects on cell growth. Together, these findings show that stable retention of specific introns can orchestrate spatial compartmentalization of RNAs within the cell; this process reveals new targets for RNA-based therapies.
Ethylene is a local modulator of jasmonate-dependent phenolamide accumulation duringManduca sextaherbivory inNicotiana attenuata
Authors: Figon Florent , Baldwin Ian T. , Gaquerel Emmanuel
Published: July 2020

Abstract

Rapid reconfigurations of intimately connected phytohormone signaling networks allow plants to tune their physiology to constantly varying ecological conditions. During insect herbivory, most of the induced changes in defense-related leaf specialized metabolites are controlled by jasmonate (JA) signaling, which, in the wild tobaccoNicotiana attenuata, recruits MYB8, a transcription factor controlling the accumulation of phenolic-polyamine conjugates (phenolamides). In this and other plant species, herbivory also locally triggers ethylene (ET) production but the outcome of the JA-ET crosstalk at the level of secondary metabolism regulation has remained superficially investigated. Here, we analyzed local and systemic herbivory-induced changes by mass spectrometry-based metabolomics in leaves of transgenic plants impaired in JA, ET and MYB8 signaling. Parsing deregulations in this factorial data-set identified a network of JA/MYB8-dependent phenolamides for which impairment of ET signaling attenuated their accumulation only in locally-damaged leaves. Further experiments revealed that ET, albeit biochemically interrelated to polyamine metabolism via the intermediateS-adenosylmethionine, does not impart on free polyamine levels, but instead significantly modulates phenolamide levels and marginally affected transcript levels in this pathway. This study identifies ET as a local modulator of phenolamide investments and provides a metabolomics data-platform to mine associations between herbivory-induced signaling and specialized metabolite groups inN. attenuata.

Summary statement

Herbivory-elicited ethylene acts as a local enhancer of the production of jasmonate/MYB8-dependent phenolamides during the defense response ofNicotiana attenuataleaves against herbivory by the lepidopteran larvaManduca sexta.
Molecular analyses reveal consistent food web structure with elevation in rainforestDrosophila- parasitoid communities
Authors: Jeffs Christopher T. , Terry J. Christopher D. , Higgie Megan , Jandová Anna , Konvičková Hana , Brown Joel J. , Lue Chia Hua , Schiffer Michele , O’Brien Eleanor K. , Bridle Jon , Hrcek Jan , Lewis Owen T.
Published: July 2020

The analysis of interaction networks across spatial environmental gradients is a powerful approach to investigate the responses of communities to global change. Using a combination of DNA metabarcoding and traditional molecular methods we built bipartiteDrosophila-parasitoid food webs from six Australian rainforest sites across gradients spanning 850 m in elevation and 5° Celsius in mean temperature. Our cost-effective hierarchical approach to network reconstruction separated the determination of host frequencies from the detection and quantification of interactions. The food webs comprised 5-9 host and 5-11 parasitoid species at each site, and showed a lower incidence of parasitism at high elevation. Despite considerable turnover in the relative abundance of hostDrosophilaspecies, and contrary to some previous results, we did not detect significant changes to fundamental metrics of network structure including nestedness and specialisation with elevation. Advances in community ecology depend on data from a combination of methodological approaches. It is therefore especially valuable to develop model study systems for sets of closely-interacting species that are diverse enough to be representative, yet still amenable to field and laboratory experiments.
Arc1 and the microbiota together modulate growth and metabolic traits inDrosophila
Authors: Keith Scott A. , Bishop Cassandra , Fallacaro Samantha , McCartney Brooke M.
Published: July 2020

Perturbations to animal-associated microbial communities (the microbiota) have deleterious effects on various aspects of host fitness, but the molecular processes underlying these impacts are poorly understood. Here we identify a novel connection between the microbiota and the neuronal factor Arc1 that affects growth and metabolism inDrosophila. We find thatArc1exhibits tissue-specific microbiota-dependent expression changes, and that germ-free flies bearing a null mutation ofArc1exhibit delayed and stunted larval growth, along with a variety of molecular, cellular, and organismal traits indicative of metabolic dysregulation. Remarkably, we show that the majority of these phenotypes can be fully suppressed by mono-association with a singleAcetobacter sp.isolate, through mechanisms involving both bacterial diet modification and live bacteria. Additionally, we provide evidence that Arc1 function in key neuroendocrine cells of the larval brain modulates growth and metabolic homeostasis under germ-free conditions. Our results reveal a novel role for Arc1 in modulating physiological responses to the microbial environment, and highlight how host-microbe interactions can profoundly impact the phenotypic consequences of genetic mutations in an animal host.

DrosophilaArc1 exhibits microbiota-dependent, tissue-specific differential expression and functionally interacts with a keyAcetobacter sp.isolate to regulate developmental growth and metabolic traits.
Segmentation of the Zebrafish Brain Vasculature from Light Sheet Fluorescence Microscopy Datasets
Authors: Kugler Elisabeth C. , Rampun Andrik , Chico Timothy J.A. , Armitage Paul A.
Published: July 2020

Light sheet fluorescent microscopy allows imaging of zebrafish vascular development in great detail. However, interpretation of data often relies on visual assessment and approaches to validate image analysis steps are broadly lacking. Here, we compare different enhancement and segmentation approaches to extract the zebrafish cerebral vasculature, provide comprehensive validation, study segmentation robustness, examine sensitivity, apply the validated method to quantify embryonic cerebrovascular volume, and examine applicability to different transgenic reporter lines. The best performing segmentation method was used to train different deep learning networks for segmentation. We found that U-Net based architectures outperform SegNet. While there was a slight overestimation of vascular volume using the U-Net methodologies, variances were low, suggesting that sensitivity to biological changes would still be obtained.

Highlights

General filtering is less applicable than Sato enhancement to enhance zebrafish cerebral vessels.

Biological data sets help to overcome the lack of segmentation gold-standards and phantom models.

Sato enhancement followed by Otsu thresholding is highly accurate, robust, and sensitive.

Direct generalization of the segmentation approach to transgenics, other than the one optimized for, should be treated with caution.

Deep learning based segmentation is applicable to the zebrafish cerebral vasculature, with U-Net based architectures outperforming SegNet architectures.

Graphical Abstract
A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis
Authors: Meijer Mandy , Agirre Eneritz , Kabbe Mukund , van Tuijn Cassandra A. , Heskol Abeer , Falcão Ana Mendanha , Corces M. Ryan , Montine Thomas J. , Chen Xingqi , Chang Howard Y. , Castelo-Branco Gonçalo
Published: July 2020

Multiple sclerosis (MS) is a disease characterized by a targeted immune attack on myelin in the central nervous system (CNS). We have previously shown that oligodendrocytes (OLs), myelin producing cells in the CNS, and their precursors (OPCs), ac-quire disease-specific transcriptional states in MS1,2. To under-stand how these alternative transcriptional programs are acti-vated in disease, we performed single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) on the OL lineage in the experimental autoimmune encephalomyeli-tis (EAE) mouse model of MS. We identified regulatory regions with increased accessibility in oligodendroglia (OLG) in EAE, some of which in the proximity of immune genes. A similar re-modeling of chromatin accessibility was observed upon treat-ment of postnatal OPCs with interferon-gamma (IFNγ), but not with dexamethasone. These changes in accessibility were not exclusive to distal enhancers, but also occurred at promoter re-gions, suggesting a role for promoters in mediating cell-state transitions. Notably, we found that a subset of immune genes al-ready exhibited chromatin accessibility in OPCs ex vivo and in vivo, suggesting a primed chromatin state in OLG compatible with rapid transitions to an immune-competent state. Several primed genes presented bivalency of H3K4me3 and H3K27me3 at promoters in OPCs, with loss of H3K27me3 upon IFNγtreatment. Inhibition of JMJD3/Kdm6b, mediating removal of H3K27me3, led to the inability to activate these genes upon IFNγtreatment. Importantly, OLGs from the adult human brain showed chromatin accessibility at immune gene loci, par-ticularly at MHC-I pathway genes. A subset of single-nucleotide polymorphisms (SNPs) associated with MS susceptibility over-lapped with these primed regulatory regions in OLG from both mouse and human CNS. Our data suggest that susceptibility for MS may involve activation of immune gene programs in OLG. These programs are under tight control at the chromatin level in OLG and may therefore constitute novel targets for immunological-based therapies for MS.
Response of soil microbial communities to mixed forests of European beech and conifers: Variations with site conditions
Authors: Lu Jing-Zhong , Scheu Stefan
Published: July 2020

Tree - soil interactions depend on environmental conditions. Planting trees may strongly impact microorganisms in particular at unfavorable site conditions, compromising the functioning of soil microorganisms. To understand the effects of tree species composition on soil microorganisms, we quantified structural and functional responses of soil microorganisms to forest types across environmental conditions using substrate-induced respiration and phospholipid fatty acid analyses. Five forest types were studied including pure stands of native European beech (Fagus sylvatica), range expanding Norway spruce (Picea abies), and non-native Douglas-fir (Pseudotsuga menziesii), as well as the two conifer - beech mixtures. We found that microbial functioning strongly depends on site conditions, in particular on soil nutrients. At nutrient-poor sites, soil microorganisms were more stressed in pure and mixed coniferous forests, especially in Douglas-fir, compared to beech forests. By contrast, microbial structure and functional indicators in beech forests varied little with site conditions, likely because beech provided high amounts of root-derived resources for microbial growth. Since soil microbial communities are sensitive to Douglas-fir, planting Douglas-fir may compromise ecosystem functioning in particular at nutrient-poor sites. Overall, root-derived resources are important for determining the structure and functioning of soil microbial communities, and soil microorganisms sensitively respond to plantations containing tree species that may differ in the provisioning of these resources.
Isolation and Molecular Characterization of Pesticide Degrading Bacteria in Polluted Soil
Authors: Sowunmi Kehinde , Shoga Suliat Morenike , Adewunmi Oluwabukola Mabel , Oriyomi Adewale Felix , Sowunmi Lukman
Published: July 2020

The authors have withdrawn this manuscript because the research paper do not stand by it findings/conclusions or acknowledge fundamental errors in the paper. Therefore, the authors do do wish this work to be cited as reference for the project. If you have any further questions, please contact the real author of the research paper via email:oyedirane@gmail.com
Comparison of long read sequencing technologies in resolving bacteria and fly genomes
Authors: Tvedte Eric S. , Gasser Mark , Sparklin Benjamin C. , Michalski Jane , Zhao Xuechu , Bromley Robin , Tallon Luke J. , Sadzewicz Lisa , Rasko David A. , Dunning Hotopp Julie C.
Published: July 2020

Background

The newest generation of DNA sequencing technology is highlighted by the ability to sequence reads hundreds of kilobases in length, and the increased availability of long read data has democratized the genome sequencing and assembly process. PacBio and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. Released in 2019, the PacBio Sequel II platform advertises substantial enhancements over previous PacBio systems.

Results

We used whole-genome sequencing data produced by two PacBio platforms (Sequel II and RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteriaEscherichia coliand the fruit flyDrosophila ananassae. Sequel II assemblies had higher contiguity and consensus accuracy relative to other methods, even after accounting for differences in sequencing throughput. ONT RAPID libraries had the fewest chimeric reads in addition to superior quantification ofE. coliplasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assemblies or combined ONT and Sequel II libraries for eukaryotic genome assemblies. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of knownE. colimethyltransferase recognition motifs in addition to undocumentedD. ananassaemotifs.

Conclusions

The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.
Evaluating tank acclimation and trial length for shuttle box temperature preference assays
Authors: Harman Adam Alexander , Fuzzen Meghan , Stoa Lisa , Boreham Douglas , Manzon Richard , Somers Christopher M. , Wilson Joanna Yvonne
Published: July 2020

Thermal preferenda are largely defined by optimal growth temperature for a species and describe the range of temperatures an organism will occupy when given a choice. Assays for thermal preferenda require at least 24 hours, which includes a long acclimation to the tank, limits throughput and thus impacts replication in the study. Three different behavioral assay experimental designs were tested to determine the effect of tank acclimation and trial length (12:12, 0:12, 2:2; hours of tank acclimation: behavioral trial) on the temperature preference of juvenile lake whitefish, using a shuttle box system. Average temperature preferences for the 12:12, 0:12, and 2:2 experimental designs were 16.10 ± 1.07 °C, 16.02 ± 1.56 °C, 16.12 ± 1.59°C respectively, with no significant differences between the experimental designs (p= 0.9337). Ultimately, length of acclimation time and trial length had no significant impact, suggesting that all designs were equally useful for studies of temperature preference.
Predicting cancer prognosis and drug response from the tumor microbiome
Authors: Hermida Leandro C. , Gertz E. Michael , Ruppin Eytan
Published: July 2020

Tumor gene expression is predictive of patient prognosis in some cancers. However, RNA- seq and whole genome sequencing data contain not only reads from host tumor and normal tissue, but also reads from the tumor microbiome, which can be used to infer the microbial abundances in each tumor. Here, we show that tumor microbial abundances, alone or in combination with tumor gene expression data, can predict cancer prognosis and drug response to some extent – microbial abundances are significantly less predictive of prognosis than gene expression, although remarkably, similarly as predictive of drug response, but in mostly different cancer-drug combinations. Thus, it appears possible to leverage existing sequencing technology, or develop new protocols, to obtain more non-redundant information about prognosis and drug response from RNA-seq and whole genome sequencing experiments than could be obtained from tumor gene expression or genomic data alone.