bluuebunny/crossref_metadata_2025 huggingface dataset:
Interpreting Deep Ensemble Learning through Radiologist Annotations for COVID-19 Detection in Chest Radiographs
Authors: Rajaraman Sivaramakrishnan , Sornapudi Sudhir , Alderson Philip O , Folio Les R , Antani Sameer K
Published: July 2020

Data-driven deep learning (DL) methods using convolutional neural networks (CNNs) demonstrate promising performance in natural image computer vision tasks. However, using these models in medical computer vision tasks suffers from several limitations, viz., (i) adapting to visual characteristics that are unlike natural images; (ii) modeling random noise during training due to stochastic optimization and backpropagation-based learning strategy; (iii) challenges in explaining DL black-box behavior to support clinical decision-making; and (iv) inter-reader variability in the ground truth (GT) annotations affecting learning and evaluation. This study proposes a systematic approach to address these limitations for COVID-19 detection using chest X-rays (CXRs). Specifically, our contribution benefits from (i) pretraining specific to CXRs in transferring and fine-tuning the learned knowledge toward improving COVID-19 detection performance; (ii) using ensembles of the fine-tuned models to further improve performance compared to individual constituent models; (iii) performing statistical analyses at various learning stages to validate our claims; (iv) interpreting learned individual and ensemble model behavior through class-selective relevance mapping (CRM)-based region of interest (ROI) localization; (v) analyzing inter-reader variability and ensemble localization performance using Simultaneous Truth and Performance Level Estimation (STAPLE) methods. We observe that: (i) ensemble approaches improved classification and localization performance; and, (ii) inter-reader variability and performance level assessment helped guide algorithm design and parameter optimization. To the best of our knowledge, this is the first study to construct ensembles, perform ensemble-based disease ROI localization, and analyze inter-reader variability and algorithm performance for COVID-19 detection in CXRs.
The First Consecutive 5000 Patients with COVID-19 in Qatar; a Nation-wide Cohort Study
Authors: Omrani Ali S. , Almaslamani Muna A. , Daghfal Joanne , Alattar Rand A. , Elgara Mohamed , Shaar Shahd H. , Ibrahim Tawheeda B. H. , Zaqout Ahmed , Bakdach Dana , Akkari Abdelrauof M. , Baiou Anas , Alhariri Bassem , Elajez Reem , Husain Ahmed A. M. , Badawi Mohamed N. , Abid Fatma Ben , Jarir Sulieman Abu , Abdalla Shiema , Kaleeckal Anvar , Choda Kris , Chinta Venkateswara R. , Sherbash Mohamed A. , Al-Ismail Khalil , Abukhattab Mohammed , Hssain Ali Ait , Coyle Peter V. , Bertollini Roberto , Frenneaux Michael P. , Khal Abdullatif Al , Al kuwari Hanan M.
Published: July 2020

Background

There are limited data on Coronavirus Disease 2019 (COVID-19) outcomes at a national level, and none after 60 days of follow up. The aim of this study was to describe national, 60-day all-cause mortality associated with COVID-19, and to identify risk factors associated with admission to an intensive care unit (ICU).

Methods

This was a retrospective cohort study including the first consecutive 5000 patients with COVID-19 in Qatar who completed 60 days of follow up by June 17, 2020. Outcomes included all-cause mortality at 60 days after COVID-19 diagnosis, and risk factors for admission to ICU.

Results

Included patients were diagnosed with COVID-19 between February 28 and April 17, 2020. The majority (4436, 88.7%) were males and the median age was 35 years [interquartile range (IQR) 28– 43]. By 60 days after COVID-19 diagnosis, 14 patients (0.28%) had died, 10 (0.2%) were still in hospital, and two (0.04%) were still in ICU. Fatal COVID-19 cases had a median age of 59.5 years (IQR 55.8–68), and were mostly males (13, 92.9%). All included pregnant women (26, 0.5%), children (131, 2.6%), and healthcare workers (135, 2.7%) were alive and not hospitalized at the end of follow up.

A total of 1424 patients (28.5%) required hospitalization, out of which 108 (7.6%) were admitted to ICU. Most frequent co-morbidities in hospitalized adults were diabetes (23.2%), and hypertension (20.7%). Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P <0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P <0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission.

Conclusions

In a relatively younger national cohort with a low co-morbidity burden, COVID-19 was associated with low all-cause mortality. Independent risk factors for ICU admission included older age, male sex, higher BMI, and co-existing diabetes or chronic kidney disease.
Space-time patterns, change, and propagation of COVID-19 risk relative to the intervention scenarios in Bangladesh
Authors: Masrur Arif , Yu Manzhu , Luo Wei , Dewan Ashraf
Published: July 2020

The novel coronavirus (COVID-19) pandemic continues to be a significant public health threat worldwide. As of mid-June 2020, COVID-19 has spread worldwide with more than 7.7 million confirmed cases and more than 400,000 deaths. The impacts are substantial particularly in developing and densely populated countries like Bangladesh with inadequate health care facilities, where COVID-19 cases are currently surging. While early detection and isolation were identified as important non-pharmaceutical intervention (NPI) measures for containing the disease spread, this may not be pragmatically implementable in developing countries primarily due to social and economic reasons (i.e. poor education, less public awareness, massive unemployment). To shed light on COVID-19 transmission dynamics and impacts of NPI scenarios – e.g. social distancing, this study conducted emerging pattern analysis using the space-time scan statistic at district and thana (i.e. a sub-district or ‘upazila’ with at least one police station) levels in Bangladesh and its capital – Dhaka city, respectively. We found that the central and south eastern regions in Bangladesh are currently exhibiting a high risk of COVID-19 transmission. Dhaka megacity remains as the highest risk “active” cluster since early April. The space-time progression of COVID-19 infection, when validated against the chronicle of government press releases and newspaper reports, suggests that Bangladesh have experienced a community level transmission at the early phase (i.e., March, 2020) primarily introduced by Bangladeshi citizens returning from coronavirus-affected countries in the Europe and the Middle East. A linkage is evident between the violation of NPIs and post-incubation period emergence of new clusters with elevated exposure risk around Bangladesh. This study provides novel insights into the space-time patterns of COVID-19 transmission dynamics and recommends pragmatic NPI implementation for reducing disease transmission and minimizing impacts in a resource-scarce country with Bangladesh as a case-study example.
The utility of established prognostic scores in COVID-19 hospital admissions: a multi-centre prospective evaluation of CURB-65, NEWS2, and qSOFA
Authors: Bradley Patrick , Frost Freddy , Tharmaratnam Kukatharmini ,   NW-CORR Collaborators, Wootton Dan Gower
Published: July 2020

Introduction

The COVID-19 pandemic is ongoing yet, due to the lack of a COVID-19 specific tool, clinicians must use pre-existing illness severity scores for initial prognostication. However, the validity of such scores in COVID-19 is unknown.

Methods

The North West Collaborative Organization for Respiratory Research (NW-CORR) performed a multi-centre prospective evaluation of adult patients admitted to hospital with confirmed COVID-19 during a two-week period in April 2020. Clinical variables measured as part of usual care at presentation to hospital were recorded, including the CURB-65, NEWS2, and qSOFA scores. The primary outcome of interest was 30-day mortality.

Results

Data were collected for 830 people with COVID-19 admitted across 7 hospitals. By 30 days, a total of 300 (36.1%) had died and 142 (17.1%) had been in ICU. All scores underestimated mortality compared to their original validation in non-COVID-19 populations, and overall prognostic performance was generally poor. Among the ‘low risk’ categories (CURB-65<2, NEWS2<5, qSOFA<2) 30-day mortality was 16.7%, 32.9% and 21.4%, respectively. Multivariable logistic regression identified features of respiratory compromise rather than circulatory collapse as most relevant prognostic variables.

Conclusion

All existing prognostic scores evaluated here underestimated adverse outcomes and performed sub-optimally in the COVID-19 setting. New prognostic tools including a focus on features of respiratory compromise rather than circulatory collapse are needed. We provide a baseline set of variables which are relevant to COVID-19 outcomes and may be used as a basis for developing a bespoke COVID-19 prognostication tool.

Key Messages

What is the key question?

Do well-established illness severity scores have prognostic value in COVID-19?

What is the bottom line?

All scores appeared to underestimate mortality in COVID-19 and prognostic performance was generally poor, and importantly could not discriminate those patients at very low risk of death within 30 days.

Why read on?

In this multi-centre prospective evaluation of CURB-65, NEWS2 and qSOFA we comprehensively evaluate score performance and also identify variables which may be of use in COVID-19 prognostication.
Higher Comorbidities and Early Death is Characteristic of Hospitalized African-American Patients with COVID-19
Authors: Gupta Raavi , Agrawal Raag , Bukhari Zaheer , Jabbar Absia , Wang Donghai , Diks John , Alshal Mohamed , Emechebe Dokpe Yvonne , Brunicardi F. Charles , Lazar Jason M. , Chamberlain Robert , Burza Aaliya , Haseeb M.A.
Published: July 2020

Background

African-Americans/Blacks have suffered higher morbidity and mortality from COVID-19 than all other racial groups. This study aims to identify the causes of this health disparity, determine prognostic indicators, and assess efficacy of treatment interventions.

Method

We performed a retrospective cohort study of clinical features and laboratory data of COVID-19 patients admitted over a five-week period at the height of the pandemic in the United States. This study was performed at an urban academic medical center in New York City, declared a COVID-only facility, serving a majority Black population

Result

Of the 1,070 consecutive patients who tested positive for COVID-19, 496 critically ill patients were hospitalized and included in the study. 88% of patients were Black; and a majority (53%) were 61-80 years old with a mean body mass index in the “obese” range. 97% had one or more comorbidities. Hypertension was the most common (84%) pre-existing condition followed by diabetes mellitus (57%) and chronic kidney disease (24%). Patients with chronic kidney disease and end-stage renal disease who received hemodialysis were found to have significantly lower mortality, then those who did not receive it, suggesting benefit from hemodialysis (11%, OR, 0.35, CI, 0.17 - 0.69 P=0.001). Age >60 years and coronary artery disease were independent predictors of mortality in multivariate analysis. Cox Proportional Hazards modeling for time to death demonstrated a significantly high ratio for COPD/Asthma, and favorable effects on outcomes for pre-admission ACE inhibitors and ARBs. CRP (180, 283 mg/L), LDH (551, 638 U/L), glucose (182, 163 mg/dL), procalcitonin (1.03, 1.68 ng/mL), and neutrophil / lymphocyte ratio (8.5, 10.0) were predictive of mortality on admission and at 48-96 hrs. Of the 496 inpatients, 48% died, one third of patients died within the first three days of admission. 54/488 patients received invasive mechanical ventilation, of which 87% died and of the remaining patients, 32% died.

CONCLUSIONS

COVID-19 patients in our predominantly Black neighborhood had higher mortality, likely due to higher prevalence of comorbidities. Early dialysis and pre-admission intake of ACE inhibitors/ARBs improved patient outcomes. Early escalation of care based on comorbidities and key laboratory indicators is critical for improving outcomes in African-American patients.
Home-based and remote exercise testing in chronic respiratory disease, during the COVID-19 pandemic and beyond: a rapid review
Authors: Holland Anne E , Malaguti Carla , Hoffman Mariana , Lahham Aroub , Burge Angela T , Dowman Leona , May Anthony K , Bondarenko Janet , Graco Marnie , Tikellis Gabriella , Lee Joanna Y. T. , Cox Narelle S
Published: July 2020

Objectives

To identify exercise tests that are suitable for home-based or remote administration in people with chronic lung disease.

Methods

Rapid review of studies that reported home-based or remote administration of an exercise test in people with chronic lung disease, and studies reporting their clinimetric properties.

Results

84 studies were included. Tests used at home were the 6-minute walk test (6MWT, 2 studies), sit-to-stand tests (STS, 5 studies), Timed Up and Go (TUG, 4 studies) and step tests (2 studies). Exercise tests administered remotely were the 6MWT (2 studies) and step test (1 study). Compared to centre-based testing the 6MWT distance was similar when performed outdoors but shorter when performed at home (2 studies). The STS, TUG and step tests were feasible, reliable (intra-class correlation coefficients >0.80), valid (concurrent and known groups validity) and moderately responsive to pulmonary rehabilitation (medium effect sizes). These tests elicited less desaturation than the 6MWT, and validated methods to prescribe exercise were not reported.

Discussion

The STS, step and TUG tests can be performed at home, but do not accurately document desaturation with walking or allow exercise prescription. Patients at risk of desaturation should be prioritised for centre-based exercise testing when this is available.
Associations between Demographic Characteristics, Perceived Threat, Perceived Stress, Coping Responses and Adherence to COVID-19 Prevention Measures among Healthcare Students in China: A Cross-Sectional Survey with Implications for the Control of COVID-19
Authors: Tang Anson Chui Yan , Kwong Enid Wai Yung , Chen Liangying , Cheng Winnie Lai Sheung
Published: July 2020

Objectives

To investigate the associations between demographic characteristics, perceived threat, perceived stress, coping responses and adherence to COVID-19 prevention measures in Chinese Healthcare students.

Design

A cross-sectional survey collecting data in Hong Kong and Fujian Province of China. Self-administered questionnaires were collected via online platform in April 2020.

Participants

A convenience and snowball sample of 2706 students aged 18 years or older and studying a healthcare programme in Hong Kong or Fujian.

Setting

Students were recruited in tertiary education institutions/universities in Hong Kong and Putian (a prefecture-level city in eastern Fujian province). The institutions offered various healthcare programmes in degree or sub-degree levels.

Main outcome measures

Compliances to social distancing and personal hygiene measures were assessed by 10-item Social Distancing Scale and 5-item Personal Hygiene Scale respectively. Path analysis was performed to identify factors associated with the compliance outcomes.

Results

The participants reported high compliances to both social distancing and personal hygiene measures. Confidence to manage the current situation, wishful thinking and empathetic responding directly predicted compliance to social distancing (β=-0.31, p<0.001; β=0.35, p=0.015; β=0.33, p<0.001 respectively) and personal hygiene measures (β==-0.16, p<0.001; β=0.21, p<0.001; β=0.16, p<0.001 respectively). Gender, geographical location, and clinical experience were the only three demographic variables having direct and/or indirect effects on social distancing and personal hygiene measures. The final model constructed demonstrated a very good fit to the data (Chi-square X2=27.27, df=17, P=0.044; X2/df=1.61; GFI=0.998, CFI=0.997, TLI=0.992, RMSEA=0.015).

Conclusions

The predictive model constructed in this study is the first one to explore factors associating with the compliance to infection control measures in healthcare students amid the COVID-19 outbreak. The findings suggest that students who are male, habituate in Hong Kong, have more clinical experience and weak confidence to manage the threat tend to have lower compliance to social distancing and personal hygiene measures. Wishful thinking, contrasting to previous studies, was first found to positively associate with adherence to COVID-19 control measures.
Early life stress dysregulates kappa opioid receptor signaling within the lateral habenula
Authors: Simmons Sarah C. , Shepard Ryan D. , Gouty Shawn , Langlois Ludovic D. , Cox Brian M. , Nugent Fereshteh S.
Published: July 2020

The lateral habenula (LHb) is an epithalamic brain region associated with value-based decision making and stress evasion through its modulation of dopamine (DA)-mediated reward circuitry. Specifically, increased activity of the LHb is associated with drug addiction, schizophrenia and stress-related disorders such as depression, anxiety and posttraumatic stress disorder. Dynorphin (Dyn)/Kappa opioid receptor (KOR) signaling is a mediator of stress response in reward circuitry. Previously, we have shown that maternal deprivation (MD), a severe early life stress, increases LHb intrinsic excitability while blunting the response of LHb neurons to extra hypothalamic corticotropin-releasing factor (CRF) signaling, another stress mediator. CRF pathways also interact with Dyn/KOR signaling. Surprisingly, there has been little study of direct KOR regulation of the LHb despite its distinct role in stress, reward and aversion processing. To test the functional role of Dyn-KOR signaling in the LHb, we utilized ex-vivo electrophysiology combined with pharmacological tools in rat LHb slices. We show that activation of KORs by a KOR agonist (U50,488) exerts differential effects on the excitability of two distinct subpopulations of LHb neurons that differ in their expression of hyperpolarization-activated cation currents (HCN, Ih). Specifically, KOR stimulation increases neuronal excitability in LHb neurons with large Ih currents (Ih+) while decreases neuronal excitability in small/negative Ih (Ih-) neurons. Additionally, we found that an intact fast-synaptic transmission is required for the effects of U50,488 on the excitability of both Ih- and Ih+ LHb neuronal subpopulations. Consistently, KOR activation also altered both glutamatergic and GABAergic synaptic transmission. While stimulation of presynaptic KORs uniformly suppressed glutamate release onto LHb neurons, we found that U50, 488 either increased or decreased GABA release. We also found that MD significantly increased immunolabeled Dyn (the endogenous KOR agonist) labeling in neuronal fibers in LHb while significantly decreased mRNA levels of KORs in LHb tissues compared to those from non-maternally deprived (non-MD) control rats. While total p38 MAPK (a downstream signaling pathway driven by KOR activation) expression was elevated in the LHb of MD rats compared to non-MD controls, we found that application of KOR-specific agonist, U50,488, onto LHb slices was still able to alter phosphorylated p38 MAPK (ph-p38) expression in MD rats similar to non-MD controls. Moreover, we found that the U50,488-mediated increase in LHb neuronal firing observed in non-MD rats was absent following MD. Altogether, this is the first demonstration of the existence of the functional Dyn/KOR signaling in the LHb that can be modulated in response to severe early life stressors such as MD.
PFN2 and NAA80 cooperate to efficiently acetylate the N-terminus of actin
Authors: Ree Rasmus , Kind Laura , Kaziales Anna , Varland Sylvia , Dai Minglu , Richter Klaus , Drazic Adrian , Arnesen Thomas
Published: July 2020

The actin cytoskeleton is of profound importance to cell shape, division, and intracellular force generation. Profilins bind to globular (G-)actin and regulate actin filament formation. Although profilins are well-established actin regulators, the distinct roles of the dominant profilin, profilin 1 (PFN1), versus the less abundant profilin 2 (PFN2) remain enigmatic. Here, we define a specific role for PFN2 as a stable interactor and regulator of the actin N-terminal acetyltransferase NAA80. PFN2 binding increases the intrinsic catalytic activity of NAA80. Furthermore, binding of PFN2 to NAA80 via its proline-rich loop promotes binding between the globular domains of actin and NAA80, and thus acetylation of actin. The majority of NAA80 is stably bound to PFN2, and we propose that this complex acetylates G-actin before it is incorporated into filaments. In conclusion, we reveal a functionally specific role of PFN2, and establish the modus operandi for NAA80-mediated actin N-terminal acetylation. Data are available via ProteomeXchange with identifier PXD020188.
Spatio-temporal control of phenylpropanoid biosynthesis by inducible complementation of a cinnamate 4-hydroxylase mutant
Authors: Kim Jeong Im , Hidalgo-Shrestha Christopher , Bonawitz Nicholas D. , Franke Rochus B. , Chapple Clint
Published: July 2020

Cinnamate 4-hydroxylase (C4H) is a cytochrome P450-dependent monooxygenase that catalyzes the second step of the general phenylpropanoid pathway. Arabidopsisreduced epidermal fluorescence 3(ref3) mutants, which carry hypomorphic mutations inC4H, exhibit global alterations in phenylpropanoid biosynthesis and have developmental abnormalities including dwarfing. Here we report the characterization of a conditional Arabidopsis C4H line (ref3-2pOpC4H), in which wild-typeC4His expressed in theref3-2background. Expression ofC4Hin plants with well-developed primary inflorescence stems resulted in restoration of fertility and the production of substantial amounts of lignin, revealing that the developmental window for lignification is remarkably plastic. Following induction ofC4Hexpression inref3-2pOpC4H, we observed rapid and significant reductions in the levels of numerous metabolites, including several benzoyl and cinnamoyl esters and amino acid conjugates. These atypical conjugates were quickly replaced with their sinapoylated equivalents, suggesting that phenolic esters are subjected to substantial amounts of turnover in wild-type plants. Furthermore, using localized application of dexamethasone toref3-2pOpC4H, we show that phenylpropanoids are not transported appreciably from their site of synthesis. Finally, we identified a defective Casparian strip diffusion barrier in theref3-2mutant root endodermis, which is restored by induction ofC4Hexpression.

Highlight

The work presented this paper provides evidence of metabolite turnover, plasticity of the developmental window for lignification, and the impact of reduced and restored cinnamate-4-hydroxylase (C4H)expression on the Casparian strip.
Prophylactic and Therapeutic Inhibition of In Vitro SARS-CoV-2 Replication by Oleandrin
Authors: Plante Kenneth S. , Plante Jessica A. , Fernandez Diana , Mirchandani Divya , Bopp Nathen , Aguilar Patricia V. , Sastry K. Jagannadha , Newman Robert A. , Weaver Scott C.
Published: July 2020

With continued expansion of the COVID-19 pandemic, antiviral drugs are desperately needed to treat patients at high risk of life-threatening disease and even to limit spread if administered early during infection. Typically, the fastest route to identifying and licensing a safe and effective antiviral drug is to test those already shown safe in early clinical trials for other infections or diseases. Here, we testedin vitrooleandrin, derived from theNerium oleanderplant and shown previously to have inhibitory activity against several viruses. Using Vero cells, we found that prophylactic oleandrin administration at concentrations down to 0.05 μg/ml exhibited potent antiviral activity against SARS-CoV-2, with an 800-fold reduction in virus production, and a 0.1 μg/ml dose resulted in a greater than 3,000-fold reduction in infectious virus production. The EC50values were 11.98ng/ml when virus output was measured at 24 hours post-infection, and 7.07ng/ml measured at 48 hours post-infection. Therapeutic (post-infection) treatment up to 24 hours after infection of Vero cells also reduced viral titers, with the 0.1 μg/ml dose causing greater than 100-fold reductions as measured at 48 hours, and the 0.05 μg/ml dose resulting in a 78-fold reduction. The potent prophylactic and therapeutic antiviral activities demonstrated here strongly support the further development of oleandrin to reduce the severity of COVID-19 and potentially also to reduce spread by persons diagnosed early after infection.

IMPORTANCE

COVID-19, a pandemic disease caused by infection with SARS-CoV-2, has swept around the world to cause millions of infections and hundreds-of-thousands of deaths due to the lack of vaccines and effective therapeutics. We tested oleandrin, derived from theNerium oleanderplant and shown previously to reduce the replication of several viruses, against SARS-CoV-2 infection of Vero cells. When administered both before and after virus infection, nanogram doses of oleandrin significantly inhibited replication by up to 3,000-fold, indicating the potential to prevent disease and virus spread in persons recently exposed to SARS-CoV-2, as well as to prevent severe disease in persons at high risk. These results indicate that oleandrin should be tested in animal models and in humans exposed to infection to determine its medical usefulness in controlling the pandemic.
Intraperitoneal oil application causes local inflammation with depletion of resident peritoneal macrophages
Authors: Alsina-Sanchis Elisenda , Mülfarth Ronja , Moll Iris , Mogler Carolin , Rodriguez-Vita Juan , Fischer Andreas
Published: July 2020

Oil is frequently used as a solvent to inject lipophilic substances into the peritoneum of laboratory animals. Although mineral oil causes chronic peritoneal inflammation, little is known whether other oils are better suited. Here we show that olive, peanut, corn or mineral oil causes xanthogranulomatous inflammation with depletion of resident peritoneal macrophages. However, there were striking differences in the severity of the inflammatory response. Peanut and mineral oil caused severe chronic inflammation with persistent neutrophil and monocyte recruitment, expansion of the vasculature and fibrosis. Corn and olive oil provoked no or only mild signs of chronic inflammation. Mechanistically, the vegetal oils were taken up by macrophages leading to foam cell formation and induction of cell death. Olive oil triggered caspase-3 cleavage and apoptosis, which facilitates the resolution of inflammation. Peanut oil and, to a lesser degree, corn oil triggered caspase-1 activation and macrophage pyroptosis, which impairs the resolution of inflammation. As such, intraperitoneal oil administration can interfere with the outcome of subsequent experiments. As a proof-of-principle, intraperitoneal peanut oil injection was compared to its oral delivery in a thioglycolate-induced peritonitis model. The chronic peritoneal inflammation due to peanut oil injection impeded the proper recruitment of macrophages and the resolution of inflammation in this peritonitis model. In summary, the data indicate that it is advisable to deliver lipophilic substances like tamoxifen by oral gavage instead of intraperitoneal injection.
Transcriptome analysis of sevoflurane exposure effects at the different brain regions
Authors: Yamamoto Hiroto , Uchida Yutaro , Chiba Tomoki , Kurimoto Ryota , Matsushima Takahide , Ishikawa Chihiro , Li Haiyan , Shiga Takashi , Muratani Masafumi , Uchida Tokujiro , Asahara Hiroshi
Published: July 2020

Backgrounds

Sevoflurane is a most frequently used volatile anaesthetics, but its molecular mechanisms of action remain unclear. We hypothesized that specific genes play regulatory roles in whole brain exposed to sevoflurane. Thus, we aimed to evaluate the effects of sevoflurane inhalation and identify potential regulatory genes by RNA-seq analysis.

Methods

Eight-week old mice were exposed to sevoflurane. RNA from four medial prefrontal cortex, striatum, hypothalamus, and hippocampus were analysed using RNA-seq. Differently expressed genes were extracted. Their gene ontology terms and the transcriptome array data of the cerebral cortex of sleeping mice were analysed using Metascape, and the gene expression patterns were compared. Finally, the activities of transcription factors were evaluated using a weighted parametric gene set analysis (wPGSA). JASPAR was used to confirm the existence of binding motifs in the upstream sequences of the differently expressed genes.

Results

The gene ontology term enrichment analysis result suggests that sevoflurane inhalation upregulated angiogenesis and downregulated neural differentiation in the whole brain. The comparison with the brains of sleeping mice showed that the gene expression changes were specific to anaesthetized mice. Sevoflurane inducedKlf4upregulation in the whole brain. The transcriptional analysis result suggests that KLF4 is a potential transcriptional regulator of angiogenesis and neural development.

Conclusions

Klf4was upregulated by sevoflurane inhalation in whole brain. KLF4 might promote angiogenesis and cause the appearance of undifferentiated neural cells by transcriptional regulation. The roles of KLF4 might be key to elucidating the mechanisms of sevoflurane induced functional modification in the brain.
The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements
Authors: Gunnels Tess , Creswell Matthew , McFerrin Janis , Whittall Justen B.
Published: July 2020

The dietary supplement industry is a growing enterprise, valued at over $100 billion by 2025 yet, a recent study revealed that up to 60% of herbal supplements may have substituted ingredients not listed on their labels, some with harmful contaminants. Substituted ingredients make rigorous quality control testing a necessary aspect in the production of supplements. Traditionally, species have been verified morphologically or biochemically, but this is not possible for all species if the identifying characteristics are lost in the processing of the material. One approach to validating plant and fungal ingredients in herbal supplements is through DNA barcoding complemented with a molecular phylogenetic analysis. This method provides an efficient, objective, rigorous and repeatable method for species identification. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample sold asG. lucidumrepresenting independent suppliers produced single, strong amplification products in the expected size-range forGanoderma. Both best-hit BLAST and molecular phylogenetic analyses using a reference panel assembled from Genbank clearly identified the predominant fungal DNA wasG. lingzhiin all seven herbal supplements. We detected variation in ITS among our samples, but all samples still fall within a large clade ofG. lingzhi. ITS is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.
TheMycobacterium tuberculosissRNA F6 modifies expression of essential chaperonins, GroEL2 and GroES
Authors: Houghton Joanna , Rodgers Angela , Rose Graham , D’Halluin Alexandre , Kipkorir Terry , Barker Declan , Waddell Simon J , Arnvig Kristine B.
Published: July 2020

Almost 140 years after the identification ofMycobacterium tuberculosisas the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of post-transcriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of theM. tuberculosissRNA, F6, and shown it to be dependent on SigF for expression, and significantly induced in starvation conditionsin vitroand in a mouse model of infection. Further exploration of F6 using anin vitrostarvation model of infection indicates that F6 affects the expression of the essential chaperonins, GroEL2 and GroES. Our results point towards a role for F6 during periods of low metabolic activity typically associated with long-term survival ofM. tuberculosisin human granulomas.
Evaluation of Micronuclei Frequency in Both Shelter and Family Cats and Dogs
Authors: Santovito Alfredo , Buglisi Martina , Scarfo’ Manuel
Published: July 2020

Each year a lot of animals are cared for in shelters in Italy. Many of these animals have received minimal or no prior healthcare. Thus, the beneficial role animal shelters play is undeniable. Nonetheless, even well-run shelters lack the necessary resources to provide adequate conditions. It is common knowledge that group-housing can increase stress levels in family cats (Felis silvestris lybica) and dogs (Canis lupus familiaris) contributing to the development of infectious diseases and/or behavioural problems.

The aim of this study is to evaluate, through the buccal micronucleus assay, the level of genomic damage in shelter cats and dogs and compare it with that of family cats and dogs. The hypothesis is that environmental conditions such as those potentially present in shelters can affect the level of genomic damage.

The study population included thirty healthy mixed breed cats and dogs, randomly sampled, with at a minimum two-year presence in a shelter. The control group consisted of thirty healthy cats and dogs living in a home environment, using age/sex matching. The micronucleus assay was performed on one thousand exfoliated buccal mucosa cells per subject and standardized protocols were used for stress score tests.

Significant differences were found between shelter and family cats and dogs in terms of micronuclei, indicating that a condition of stress found in sheltered cats may increase the levels of genomic damage. Conversely, no significant differences in the frequency of micronuclei were found between the sexes, as well as no correlation was found between age and the frequencies of the used genomic markers.
Modeling gene regulation in response to wounding: temporal variations, hormonal variations, and specialized metabolism pathways induced by wounding
Authors: Moore Bethany M. , Lee Yun Sun , Grotewold Erich , Shiu Shin-Han
Published: July 2020

Plants respond to wounding stress by changing gene expression patterns and inducing jasmonic acid (JA), as well as other plant hormones. This includes activating some specialized metabolism pathways, including the glucosinolate pathways, in the case ofArabidopsis thaliana. We model how these responses are regulated by using machine learning to incorporate putative cis-regulatory elements (pCREs), known transcription factor binding sites from literature,in-vitroDNA affinity purification sequencing (DAP-seq) and DNase I hypersensitive sites to predict gene expression for genes clustered by their wound response using machine learning. We found temporal patterns where regulatory sites and regions of open chromatin differed between clusters of genes up-regulated at early and late wounding time points as well as clusters where JA response was induced relative to clusters where JA response was not induced. Overall, we identified pCREs that improved model predictions of expression clusters over known binding sites. We discovered 4,255 pCREs related to wound response at different time points and 2,569 pCREs related to differences between JA-induced and non-JA induced wound response. In addition, pCREs found to be important at different wounding time points were mapped to the promoters of genes in a glucosinolate biosynthesis pathway indicating regulation of this pathway under wounding stress. Finally, we experimentally validated a predicted cis-regulatory element, CCGCGT, showing that knock-out via CRISPR-Cas9 reduces gene expression in response to wounding.
In situgeneration of RNA complexes for synthetic molecular strand displacement circuits in autonomous systems
Authors: Bae Wooli , Stan Guy-Bart V. , Ouldridge Thomas E.
Published: July 2020

Synthetic molecular circuits implementing DNA or RNA strand-displacement reactions can be used to build complex systems such as molecular computers and feedback control systems. Despite recent advances, application of nucleic acid-based circuitsin vivoremains challenging due to a lack of efficient methods to produce their essential components – multi-stranded complexes known as “gates” –in situ, i.e. in living cells or other autonomous systems. Here, we propose the use of naturally occurring self-cleaving ribozymes to cut a single-stranded RNA transcript into a gate complex of shorter strands, thereby opening new possibilities for the autonomous and continuous production of RNA strands in a stoichiometrically and structurally controlled way.
Transcripts of vaccinia virus postreplicative genes do not contain a 5’ methylguanosine cap
Authors: Vopálenský Václav , Sýkora Michal , Mělková Zora , Mašek Tomáš , Pospíšek Martin
Published: July 2020

Vaccinia virus (VACV) is a prototypical poxvirus originally used for eradication of smallpox. Investigation into VACV mRNAs carried out almost half a century ago substantially contributed to the fundamental discovery of the 5’ mRNA cap, a hallmark of all eukaryotic and many viral mRNAs. VACV research also facilitated the identification and understanding of the general mechanism of 5’ mRNA cap synthesis. We characterized the VACV transcripts at the individual mRNA molecule level and found that vaccinia postreplicative mRNAs, containing nontemplated 5’ poly(A) leaders, surprisingly lack the 5’ cap structurein vivo. We also show that the lengths of the nontemplated leaders and the presence or absence of cap structures at the 5’ mRNA ends are controlled by the initiator sequence of the VACV postreplicative promoters.

One Sentence Summary

The promoter sequence determines the synthesis of the 5’ cap and poly(A) leaders in vaccinia virus postreplicative mRNAs.
Neural tube closure requires the endocytic receptor Lrp2 and its functional interaction with intracellular scaffolds
Authors: Kowalczyk Izabela , Lee Chanjae , Schuster Elisabeth , Hoeren Josefine , Trivigno Valentina , Riedel Levin , Görne Jessica , Wallingford John B. , Hammes Annette , Feistel Kerstin
Published: July 2020

Recent studies have revealed that pathogenic mutations in the endocytic receptor LRP2 in humans are associated with severe neural tube closure defects (NTDs) such as anencephaly and spina bifida. Here, we combined analysis of neural tube closure in mouse and in the African Clawed FrogXenopus laevisto elucidate the etiology of Lrp2-related NTDs.Lrp2loss-of-function (LOF) impaired neuroepithelial morphogenesis, culminating in NTDs that impeded anterior neural plate folding and neural tube closure in both model organisms. Loss of Lrp2 severely affected apical constriction as well as proper localization of the core planar cell polarity (PCP) protein Vangl2, demonstrating a highly conserved role of the receptor in these processes essential for neural tube formation. In addition, we identified a novel functional interaction of Lrp2 with the intracellular adaptor proteins Shroom3 and Gipc1 in the developing forebrain. Our data suggest that during neurulation, motifs within the intracellular domain of Lrp2 function as a hub that orchestrates endocytic membrane removal for efficient apical constriction as well as PCP component trafficking in a temporospatial manner.

Summary statement

Analysis of neurulation in mouse andXenopusreveals novel roles for Lrp2-mediated endocytosis in orchestrating apical constriction and planar cell polarity essential for neural tube closure.
Exposure to a mixture of BMAA and MCLR synergistically modulates behavior in larval zebrafish while exacerbating molecular changes related to neurodegeneration
Authors: Martin Rubia M. , Bereman Michael S. , Marsden Kurt C.
Published: July 2020

Exposure to toxins produced by cyanobacteria (i.e., cyanotoxins) is an emerging health concern due to their increased occurrence and previous associations with neurodegenerative disease including amyotrophic lateral sclerosis (ALS). The objective of this study was to evaluate the neurotoxic effects of a mixture of two co-occurring cyanotoxins, β-methylamino-L-alanine (BMAA) and microcystin leucine and arginine (MCLR), using the larval zebrafish model. We combined high-throughput behavior based toxicity assays with discovery proteomic techniques to identify behavioral and molecular changes following 6 days of exposure. While neither toxin caused mortality, morphological defects, or altered general locomotor behavior in zebrafish larvae, both toxins increased acoustic startle sensitivity in a dose-dependent manner by at least 40% (p<0.0001). Furthermore, startle sensitivity was enhanced by an additional 40% in larvae exposed to the BMAA/MCLR mixture relative to those exposed to the individual toxins. Supporting these behavioral results, our proteomic analysis revealed a 4-fold increase in the number of differentially expressed proteins (DEPs) in the mixture exposed group. Additionally, prediction analysis reveals activation and/or inhibition of 8 enriched canonical pathways (enrichment p-value<0.01; z-score≥|2|), including ILK, Rho Family GTPase, RhoGDI, and calcium signaling pathways, which have been implicated in neurodegeneration. We also found that expression of TDP-43, of which cytoplasmic aggregates are a hallmark of ALS pathology, was significantly upregulated by 5.7-fold following BMAA/MCLR mixture exposure. Together, our results emphasize the importance of including mixtures of cyanotoxins when investigating the link between environmental cyanotoxins and neurodegeneration as we reveal that BMAA and MCLR interactin vivoto enhance neurotoxicity.
Re-exposure to a sensorimotor perturbation produces opposite effects on explicit and implicit learning processes
Authors: Avraham Guy , Morehead J Ryan , Kim Hyosub E , Ivry Richard B
Published: July 2020

The motor system demonstrates an exquisite ability to adapt to changes in the environment, and to quickly reset when these changes prove transient. If similar environmental changes are encountered in the future, learning may be faster, a phenomenon known as savings. In studies of sensorimotor learning, a central component of savings is attributed to the explicit recall of the task structure and appropriate compensatory strategies. Whether implicit adaptation also contributes to savings remains subject to debate (Leow et al., 2020; Yin and Wei, 2020). We tackled this question by measuring, in parallel, explicit and implicit adaptive responses in a visuomotor rotation task, employing a protocol that typically elicits savings. While the initial rate of learning was faster in the second exposure to the perturbation, an analysis decomposing the two processes showed the benefit to be solely associated with explicit re-aiming. Surprisingly, we found a significant decrease after relearning in aftereffect magnitudes during no-feedback trials, a direct measure of implicit adaptation. In a second experiment, we isolated implicit adaptation using clamped visual feedback, a method known to eliminate the contribution of explicit learning processes. Consistent with the results of the first experiment, participants exhibited a marked reduction in the adaptation function, as well as an attenuated aftereffect when re-learning from the clamped feedback. Motivated by these results, we re-analyzed data from prior studies and observed a consistent, yet unappreciated pattern of attenuation of implicit adaptation during relearning. These results indicate that explicit and implicit sensorimotor processes exhibit opposite effects upon relearning: Explicit learning shows savings, while implicit adaptation becomes attenuated.
In situ temperature profile measurements with high-energy X-rays as a probe of optical floating zone crystal growth environment
Authors: Denney Jonathan J. , Wang Yusu , Corrao Adam A. , Huang Guanglong , Montiel David , Zhong Hui , Dooryhee Eric , Thornton Katsuyo , Khalifah Peter G.
Published: July 2020

The ability of optical floating zone (OFZ) furnaces to rapidly produce large single crystals of complex emerging materials has had a transformative effect on many scientific fields that require samples of this type. However, the crystal growth process within the OFZ furnace is not well understood owing to the challenges involved in monitoring the high-temperature crystal growth process. Novel beamline-compatible optical furnaces that approximate the inhomogeneous growth environment within an OFZ furnace have been fabricated and tested in high-energy synchrotron beamlines. It is demonstrated that temperature profiles can be effectively extracted from powder diffraction data collected on polycrystalline ceramic rods heated at their tip. Furthermore, these measured temperature profiles can be accurately reproduced using a heat-transfer model that accounts for solid-state thermal conduction, partial sample lamp power absorption, convective air cooling and radiative cooling, allowing key thermal parameters such as thermal conductivity to be extracted from experimental data.
The impact of SFAS 157 on fair value accounting and future bank performance
Authors: Ehalaiye Dimu , Tippett Mark , van Zijl Tony
Published: July 2020

Purpose

The purpose of this paper is to investigate whether levels-classified fair values of US banks based on SFAS 157: Fair Value Measurements, as recognised in the quarterly financial statements of the banks over the period from 2008 until 2015, have predictive value in relation to the banks’ future financial performance measured by operating cash flows and earnings over a three-quarter horizon period. In addition, we consider whether the global financial crisis (GFC) impacted the relationship between SFAS 157–based levels‐classified fair values and bank future financial performance.

Design/methodology/approach

We develop hypotheses connecting the net levels-classified bank fair values based on SFAS 157 with banks’ future financial performance. We test the hypotheses by estimating three-period quarters’ ahead forecasting models. We also use these models to test for the impact of the GFC on the relationship between the fair values and future financial performance.

Findings

Our findings suggest that the levels-classified net fair values based on SFAS 157 have predictive value in relation to future cash flows for banks. There is significant variation, across the levels, in the predictive value of levels-classified net fair values for future performance. Our findings indicate that the GFC has limited impact on the predictive value for cash flows, but the GFC had a significant adverse impact on earnings, and, with allowance for the effect of the GFC, the Level 2 net fair values have predictive value for the future earnings.

Originality/value

The study provides the first direct empirical evidence on the relationship between the SFAS 157 levels-classified quarterly bank fair values recognised in publicly available financial statements and banks’ future performance. Our results are consistent with the findings from earlier research (Ehalaiye et al., 2017) using annual data disclosed in the supplementary notes to the financial statements of US banks based on SFAS 107. The study, makes a significant contribution to the question of frequency of reporting and to the disclosure vs recognition debate. The study has implications for policy makers, regulators and accounting standards setters such as the Securities and Exchange Commission and the Financial Accounting Standards Board in evaluating the use of fair value measurement in financial reporting.