bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between collapse and serum creatinine and electrolyte concentrations in marathon runners: a 9-year retrospective study
Authors: Fitzpatrick Daniel , Walter Edward , Leckie Todd , Richardson Alan , Stacey Mike , Hunter Alex , Short Steve , Hill Neil , Woods David , Grimaldi Rachael , Galloway Rob , Hodgson Luke
Published: September 2020

Objective

Abnormal biochemical measurements have previously been described in runners following marathons. The incidence of plasma sodium levels outside the normal range has been reported as 31%, and the incidence of raised creatinine at 30%. This study describes the changes seen in electrolytes and creatinine in collapsed (2010–2019 events) and noncollapsed (during the 2019 event) runners during a UK marathon.

Methods

Point-of-care sodium, potassium, urea and creatinine estimates were obtained from any collapsed runner treated by the medical team during the Brighton Marathons, as part of their clinical care, and laboratory measurements from control subjects.

Results

Results from 224 collapsed runners were available. Serum creatinine was greater than the normal range in 68.9%. About 6% of sodium results were below, and 3% above the normal range, with the lowest 132 mmol/l. Seventeen percent of potassium readings were above the normal range; the maximum result was 8.4 mmol/l, but 97% were below 6.0 mmol/l. In the control group, mean creatinine was significantly raised in both the collapse and control groups, with 55.4% meeting the criteria for acute kidney injury, but had resolved to baseline after 24 h. Sodium concentration but not the potassium was significantly raised after the race compared with baseline, but only 15% were outside the normal range.

Conclusion

In this study, incidence of a raised creatinine was higher than previously reported. However, the significance of such a rise remains unclear with a similar rise seen in collapsed and noncollapsed runners, and resolution noted within 24 h. Abnormal sodium concentrations were observed infrequently, and severely abnormal results were not seen, potentially reflecting current advice to drink enough fluid to quench thirst.
Influence of previous coronary artery bypass grafting in the difficulty of acute coronary syndrome diagnosis
Authors: Miró Òscar , Martínez-Nadal Gemma , Koechlin Luca , Coll-Vinent Blanca , Gil Víctor , Aguiló Sira , Galicia Miguel , García-Martínez Ana , Ortega Mar , Strebel Ivo , Ayala Pedro López , Gualandro Danielle M. , Boeddinghaus Jasper , Nestelberger Thomas , Bragulat Ernest , Sánchez Miquel , Müller Christian , López-Barbeito Beatriz
Published: September 2020

Objectives

To investigate whether the diagnosis of acute coronary syndrome (ACS) in coronary artery bypass grafting (CABG) patients with chest pain (CP) is more difficult based on the initial clinical and electrocardiogram (ECG) findings.

Methods

We included consecutive CP patients attended at a single emergency department (ED) during a 10-year period. CABG status and the final diagnosis of ACS were considered as stated in the ED discharge report. We evaluated the frequency of 21 CP characteristics (CPC) and four ECG signatures, their individual and collective association with ACS, and ED length of stay (LOS) in CABG and non-CABG patients.

Results

We included 34 429 patients [median age: 61 years; female: 41.8%; CABG: 2204 patients (6.4%)], and ACS was diagnosed in 6727 (19.5%; CABG/non-CABG 37.2%/18.3%; P < 0.001). CABG patients more frequently had CPC and ECG findings typically associated with ACS, but their final association with ACS was weaker than in non-CABG patients (only significant after adjustment for attendant diaphoresis, throat irradiation, ST-segment elevation and T-wave inversion). The collective discriminative capacity was significantly lower in CABG patients (area under the curve 0.710 vs. 0.793; P < 0.001), even after adjustment (0.708 vs. 0.790; P < 0.001). ED LOS was longer for CABG patients, overall (P < 0.001) and for patients diagnosed with ACS (P = 0.008) and non-ACS (P < 0.001), but these differences disappeared after adjustment.

Conclusion

CABG substantially reduces the diagnostic performance of CPC and ECG findings to suggest ACS. A longer LOS in the ED in CABG patients is more related to their baseline characteristics than to CABG itself.
FUS-NFATC2 or EWSR1-NFATC2 Fusions Are Present in a Large Proportion of Simple Bone Cysts
Authors: Pižem Jože , Šekoranja Daja , Zupan Andrej , Boštjančič Emanuela , Matjašič Alenka , Mavčič Blaž , Contreras Juan A. , Gazič Barbara , Martinčič David , Snoj Žiga , Limpel Novak Katarina A. , Salapura Vladka
Published: September 2020

A simple bone cyst (SBC) is a benign bone lesion of unknown etiology. It can be differentiated from an aneurysmal bone cyst (ABC) by radiologic and histopathologic features, as well as by the absence of fusions of the USP6 gene characteristic of an ABC. In an attempt to differentiate between ABC and SBC in a recurrent bone cyst, we performed targeted RNA sequencing and found an EWSR1-NFATC2 fusion and no fusion of the USP6 gene. We subsequently analyzed additional 10 cysts, consistent with SBCs after radiologic-pathologic correlation, for the presence of an NFATC2 gene fusion, by targeted RNA sequencing, reverse-transcription polymerase chain reaction (RT-PCR) and Sanger sequencing, and fluorescent in situ hybridization. Targeted RNA sequencing showed a FUS-NFATC2 fusion in 4 of 11 SBCs and an EWSR1-NFATC2 fusion in 2 of 11 SBCs. No fusion was identified in 3 SBCs and the analysis was not successful in 2 SBCs because of the low quantity or poor quality of isolated RNA. All the 6 fusions detected by targeted RNA sequencing were confirmed by RT-PCR and Sanger sequencing, and 5 of the 6 fusions by fluorescent in situ hybridization. An additional FUS-NFATC2 fusion was identified by RT-PCR, Sanger sequencing, and fluorescent in situ hybridization in 1 of the 3 cases negative for fusions by targeted RNA sequencing. At least a large subset of SBCs represents cystic neoplasms characterized by FUS-NFATC2 or EWSR1-NFATC2 fusions, which also define a group of distinct, rare “Ewing-like” sarcomas that predominantly arise in long bones. Our results provide additional evidence of the existence of benign lesions with FUS-NFATC2 or EWSR1-NFATC2 fusions. Although they can recur locally in a nondestructive manner, their clinical course and possible relation to sarcoma with EWSR1-NFATC2 or FUS-NFATC2 fusion remains to be elucidated.
Prospective Exploratory Experience With Bivalirudin Anticoagulation in Pediatric Extracorporeal Membrane Oxygenation
Authors: Ryerson Lindsay M. , Balutis Kelsey R. , Granoski Donald A. , Nelson Lee-Ann R. , Massicotte M. Patricia , Lequier Laurance L. , Bauman Mary E.
Published: September 2020

Objectives:

Objective of this study was to determine if bivalirudin resulted in less circuit interventions than unfractionated heparin. A secondary objective was to examine associations between bivalirudin dose and partial thromboplastin time, international normalized ratio, and activated clotting time.

Design:

Prospective observational.

Setting:

Medical-surgical and cardiac PICUs.

Patients:

Neonatal and pediatric extracorporeal membrane oxygenation patients who received bivalirudin anticoagulation.

Interventions:

None.

Measurements and Main Results:

Twenty extracorporeal membrane oxygenation runs in 18 patients used bivalirudin; 90% were venoarterial. Median (interquartile range) age was 4.5 months (1.6–35 mo). Thirteen patients (72%) had an underlying cardiac diagnosis. Of the 20 runs using bivalirudin, 16 (80%) were initially started on unfractionated heparin and transitioned to bivalirudin due to ongoing circuit thrombosis despite therapeutic anti-Xa levels (n= 13), ongoing circuit thrombosis with unfractionated heparin greater than or equal to 40 U/kg/hr (n= 2), or absence of increase in ACT after bolus of 100 U/kg of unfractionated heparin and escalation of unfractionated heparin infusion (n= 1). Initial bivalirudin dose ranged from 0.2 to 0.5 mg/kg/hr; no bolus doses were used. Median (range) bivalirudin dose was 0.9 mg/kg/hr (0.15–1.6 mg/kg/hr). Median (interquartile range) time on extracorporeal membrane oxygenation was 226.5 hours (150.5–393.0 hr) including 84 hours (47–335 hr) on bivalirudin. Nonparametric results are as follows: the rate of circuit intervention was significantly lower in patients on bivalirudin than on unfractionated heparin (median [interquartile range]: 0 [0–1] and 1 [1–2], respectively; Wilcoxonp= 0.0126). Bivalirudin dose was correlated to PTT (rs= 0.4760;p< 0.0001), INR (rs= 0.6833;p< 0.0001), and ACT (rs= 0.6161;p< 0.0001). Four patients had a significant bleeding complication on bivalirudin. Survival to hospital discharge was 56%.

Conclusions:

Bivalirudin appears to be a viable option for systemic anticoagulation in pediatric extracorporeal membrane oxygenation patients who have failed unfractionated heparin, but questions remain namely its optimal monitoring strategy. This pilot study supports the need for larger prospective studies of bivalirudin in pediatric extracorporeal membrane oxygenation, particularly focusing on meaningful monitoring variables.
Significant Loss of Macronutrients During Passage Through Feeding Tube: An Observational Study
Authors: Moran-Lev Hadar , Azaiza Muhammad , Mangel Laurence , Mimouni Francis B. , Mandel Dror , Lubetzky Ronit
Published: September 2020

Objective:

Feeding infants born before week 34 of gestation is based mainly on providing nutrition directly to the gastrointestinal tract through a nasogastric tube. Little is known about the impact of formulas passage through nasogastric tube on their macronutrient content. The aim of our study was to evaluate changes in macronutrient content of various formulas after transfer through a feeding tube.

Methods:

Eleven frequently used formulas were chosen. Ten consecutive measurements were performed for each formula. Simulated real-life practice tube feeding was performed by using an infusion pump connected to a feeding tube. A Human Milk Analyzer, using an infrared spectroscopy method, was used to compare the preinfusion and postinfusion macronutrient contents of the different formulas.

Results:

A total of 220 measurements were performed. Variations in at least one macronutrient were observed in 5 out of 10 formulas. Fat and energy content were modified in 1 preterm formula.

Conclusions:

Changes in the macronutrient content after tube feeding transfer were observed for some infant formulas, including those designed for very low birth weight infants. These alterations might relate to specific formulation of each formula. The biological significance of our results to the very low birth weight infants should be studied further.
Protein-Losing Enteropathy in the Setting of Iron Deficiency Anemia: A Case Series
Authors: Tracy Michaela S. , Yasuda Jessica L. , Rufo Paul A.
Published: September 2020

Protein-losing enteropathy (PLE) in the setting of severe iron deficiency anemia (IDA) and excessive cow milk intake is an uncommonly recognized phenomenon. Here, we describe a series of 7 toddlers who presented for evaluation of edema in the setting of excessive cow milk intake between November 2016 and January 2019. Laboratory studies in each patient were consistent with IDA and hypoalbuminemia with evidence of PLE. Diagnostic evaluation and treatment of each patient differed, although all were instructed to restrict cow milk and provided with oral iron supplementation. The edema had resolved, and the IDA had improved in all 7 patients by the time of their follow-up outpatient appointments. Iron deficiency and PLE should be considered in patients who present with anasarca.
Opportunities and challenges for physical rehabilitation with indigenous populations
Authors: Lin Ivan , Coffin Juli , Bullen Jonathan , Barnabe Cheryl
Published: September 2020

Indigenous peoples in colonised countries internationally experience a disproportionately high burden of disease and disability. The impact of many of these conditions, such as musculoskeletal pain, can be ameliorated by participating in physical rehabilitation. However, access by Indigenous peoples to physical rehabilitation is low. Overcoming barriers for Indigenous peoples to access high-quality, effective, culturally secure physical rehabilitation should be a priority. Physical rehabilitation outcomes for Indigenous peoples can be enhanced by addressing health system, health service, and individual clinician-level considerations. System-level changes include a greater commitment to cultural security, improving the funding of physical rehabilitation to Indigenous communities, building the Indigenous physical rehabilitation workforce, and developing and using Indigenous-identified indicators in quality improvement. At the health service level, physical rehabilitation should be based within Indigenous health services, Indigenous people should be employed as physical rehabilitation professionals or in allied roles, and cultural training and support provided to the existing physical rehabilitation workforce. For clinicians, a focus on cultural development and the quality of communication is needed. Indigenous ill-health is complex and includes societal and social influences. These recommendations offer practical guidance toward fair, reasonable, and equitable physical rehabilitation outcomes for Indigenous peoples.
Comparison of Efficiencies Between Shear Wave Elastography, Fine-Needle Aspiration Biopsy and American College of Radiology Thyroid Imaging Reporting and Data System Scoring System in Determining the Malignity Potential of Solid Thyroid Nodules
Authors: Yavuz Alpaslan , Akbudak İbrahim , Üçler Rifki , Özgökçe Mesut , Arslan Harun , Batur Abdussamed
Published: September 2020

We aimed to evaluate the efficiencies of quantitative shear-wave elastography, fine-needle aspiration (FNA) biopsy and American College of Radiology (ACR)-thyroid imaging reporting and data system (TIRADS) scoring system in determining the malignity potential of solid thyroid nodules. In period between September 2014 and January 2016, 191 solid thyroid nodules of 189 patients were enrolled in this study. The mean shear wave velocities of the nodules were recorded by acoustic radiation force impulse method. All nodules were classified according to ACR-TIRADS scoring system and underwent FNA procedure. The cytopathologic results (after FNA) were benign in nature, atypical-cytology/suspiciously malign and highly suspicious of malignity in 117, 28, and 21 nodules, respectively. The specimen from FNA was insufficient in 25 nodules. Thirty-four nodules of 33 enrolled patients were operated, and the efficiencies of shear wave elastography, FNA, and ACR-TIRADS procedures were statistically analyzed; relying on the histopathologic results, the shear-wave elastography had 83.3% sensitivity, 93.7% specificity (with a cutoff value of 2,74 m/s), the FNA had 94.4% sensitivity, 87.5% specificity, and ACR-TIRADS had 88.2% sensitivity, 94.1 specificity in determining malignant tyroid nodules (P < 0.005). Quantitative shear wave elastography is concluded to be an effective, noninvasive, and practical imaging modality with a lesser sensitivity and specificity values than TIRADS unless a lower sensitivity but a higher specificity values than FNA (93.7% vs 87.5%) in considering the malignity potential of solid thyroid nodules.
Correlation Between the Warrior/Worrier Gene on Post Burn Pruritus and Scarring: A Prospective Cohort Study
Authors: Oh Jamie , Fernando Amali , Muffley Lara , Honari Shari , Gibran Nicole S.
Published: September 2020

Introduction:

Associations between genetic variation and clinical conditions suggest that single nucleotide polymorphisms (SNPs) might correlate with postburn outcomes. COMT modulates catecholamine metabolism, and polymorphisms within the rs4680 allele result in variable enzyme activity. Catechol-amines are known to modulate the inflammatory process and may affect scar formation. The aim of this study was to determine whether variants in the rs4680 SNP of the COMT gene are associated with post-burn pruritus and scarring.

Methods:

Adult burn patients, admitted between 2007 and 2017, with deep partial-thickness burns or delayed healing provided blood samples for genotyp-ing and self-reported itch scores within 1 year of injury. Scarring was measured using the Vancouver Scar Scale (VSS). Itch scores ≥ 4 and VSS scores >7 were considered severe. Genomic deoxyribonucleic acid was genotyped for the rs4680 SNP using realtime polymerase chain reaction (PCR).

Results:

Median itch and VSS scores were highest for GG homozygotes and lowest for AA homozygotes. This difference was statistically significant for VSS score (P < 0.0001) and approached significance for itch (P = 0.052). After accounting for confounding variables, including race/ethnicity, age, sex, and burn size, the GG homozygotes demonstrated worse scarring (odds ratio 1.88, P = 0.005) compared to AG heterozygotes whereas the AA homozygotes trended towards a protective effect against scarring (odds ratio 0.71, P = 0.10). itch did not demonstrate a statistically significant difference between rs4680 genotype.

Conclusions:

Our analysis identifies a trend between COMT genotype with scarring, with rs4680 genetic variation constituting an independent risk factor for VSS score.
Pro-IL-1β Is an Early Prognostic Indicator of Severe Donor Lung Injury During Ex Vivo Lung Perfusion
Authors: Major Triin , Ball Alexandra L. , Stone John P. , Edge Rebecca J. , Lopez-Castejon Gloria , Sjöberg Trygve , Andreasson Anders , Brough David , Steen Stig , Fisher Andrew J. , Fildes James E.
Published: September 2020

Background.

Ex vivo lung perfusion (EVLP) is used to evaluate and recondition extended criteria donor lungs for transplantation. Interleukin-1β (IL-1β) has been identified as a prognostic indicator of nonrecovery during EVLP. This may be an effect of inflammasome activation or cellular necrosis following donation and graft preservation. Delineating the mechanism of IL-1β release is required.

Methods.

The inactive intracellular precursor molecule, pro-IL-1β, was characterized along with the pro-IL-1β processing enzyme, caspase-1, in the perfusate of n = 20 human lungs that had undergone EVLP (n = 10 lungs that failed to recover and were discarded versus n = 10 lungs that reconditioned and were transplanted). In an experimental porcine model, n = 8 lungs underwent EVLP and were randomized to receive either a specific NLRP3 inflammasome inhibitor or control.

Results.

Significant increases in pro-IL-1β and caspase-1 were observed in the perfusate from human lungs that did not recondition during EVLP compared with those that successfully reconditioned and were used for transplantation. Within the porcine EVLP, NLRP3 inflammasome inhibition reduced IL-1β within the perfusate compared with controls, but this had no impact on lung function, hemodynamics, or inflammation.

Conclusions.

Our data suggest that pro-IL-1β is passively released following cellular necrosis of the donor lung.
SCOAT-Net: A Novel Network for Segmenting COVID-19 Lung Opacification from CT Images
Authors: Zhao Shixuan , Li Zhidan , Chen Yang , Zhao Wei , Xie Xingzhi , Liu Jun , Zhao Di , Li Yongjie
Published: September 2020

The new coronavirus disease 2019 (COVID19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide at a rapid rate. There is no clinically automated tool to quantify the infection of COVID-19 patients. Automatic segmentation of lung opacification from computed tomography (CT) images provides excellent potential, which is of great significance for judging the disease development and treatment response of the patients. However, the segmentation of lung opacification from CT slices still faces some challenges, including the complexity and variability features of the opacity regions, the small difference between the infected and healthy tissues, and the noise of CT images. Besides, due to the limited medical resources, it is impractical to obtain a large amount of data in a short time, which further hinders the training of deep learning models. To answer these challenges, we proposed a novel spatial and channel-wise coarse-to-fine attention network (SCOAT-Net) inspired by the biological vision mechanism, which is for the segmentation of COVID-19 lung opacification from CT Images. SCOAT-Net has the spatial-wise attention module and the channel-wise attention module to attract the self-attention learning of the network, which serves to extract the practical features at the pixel and channel level successfully. Experiments show that our proposed SCOAT-Net achieves better results compared to state-of-the-art image segmentation networks.
Natrix: A Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads
Authors: Welzel Marius , Lange Anja , Heider Dominik , Schwarz Michael , Freisleben Bernd , Jensen Manfred , Boenigk Jens , Beisser Daniela
Published: September 2020

Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires effcient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an effcient workflow management system. We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix).
Which waters hydrate best? A study using brine-shrimp cysts (Artemia franciscana)
Authors: Ye Tao , Pollack Gerald H.
Published: September 2020

Hydration plays a particularly important role in health maintenance and general well-being. A wide assortment of drinking waters are currently available on the market. However, their ability to hydrate may vary. For studying hydration, a useful organism may be the cysts of brine shrimp. Those cysts may remain dehydrated and functionless for years, but regain function once hydrated. In this study, we first determined the optimal factors for assessing hydration in the brine-shrimp model, including aeration method and flow rate, salinity, and temperature. Various kinds of water, including tap water, bottled water, and water containing health-promoting agents, were tested by using this new method to evaluate their ability to hydrate. Tap water showed weak hydration, while some bottled waters (e.g., Kirkland Signature Purified Water) hydrated more effectively. Mineral water, such as Fiji water, was found to be a desirable option to maintain adequate and lasting hydration.

Graphic abstract
Evidence for and level of herd immunity against SARS-CoV-2 infection: the ten-community study
Authors: Jeremijenko Andrew , Chemaitelly Hiam , Ayoub Houssein H. , Hassan Abdulla Moza Abdellatif , Abou-Samra Abdul-Badi , Al Ajmi Jameela Ali A.A. , Al Ansari Nasser Ali Asad , Kanaani Zaina Al , Khal Abdullatif Al , Kuwari Einas Al , Al-Mohammed Ahmed , Al Molawi Naema Hassan Abdulla , Naomi Huda Mohamad Al , Butt Adeel A. , Coyle Peter , El Kahlout Reham Awni , Gillani Imtiaz , Kaleeckal Anvar Hassan , Masoodi Naseer Ahmad , Thomas Anil George , Nafady-Hego Hanaa , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Younes Nourah B M , Abdul Rahim Hanan F. , Yassine Hadi M. , Al Kuwari Mohamed G. , Al Romaihi Hamad Eid , Al Thani Sheikh Mohammad , Bertollini Roberto , Abu-Raddad Laith J.
Published: September 2020

Background

Qatar experienced a large severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic that disproportionately affected the craft and manual workers (CMWs) who constitute 60% of the population. This study aimed to investigate level of immunity in communities within this population as well as infection exposure required to achieve herd immunity.

Methods

Anti-SARS-CoV-2 seropositivity was assessed in ten CMW communities between June 21 and September 9, 2020. PCR positivity, infection positivity (antibody and/or PCR positive), and infection severity rate were also estimated. Associations with anti-SARS-CoV-2 positivity were investigated using regression analyses.

Results

Study included 4,970 CMWs who were mostly men (95.0%) and <40 years of age (71.5%). Seropositivity ranged from 54.9% (95% CI: 50.2-59.4%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean seropositivity across all communities was 66.1% (95% CI: 61.5-70.6%). PCR positivity ranged from 0.0% to 10.5% (95% CI: 7.4-14.8%) in the different CMW communities. Pooled mean PCR positivity was 3.9% (95% CI: 1.6-6.9%). Median cycle threshold (Ct) value was 34.0 (range: 15.8-37.4)—majority (79.5%) of PCR-positive individuals had Ct value >30 indicative of earlier rather than recent infection. Infection positivity (antibody and/or PCR positive) ranged from 62.5% (95% CI: 58.3-66.7%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean infection positivity was 69.5% (95% CI: 62.8-75.9%). Only five infections were ever severe and one was ever critical—an infection severity rate of 0.2% (95% CI: 0.1-0.4%).

Conclusions

Based on an extended range of epidemiological measures, active infection is rare in these communities with limited if any sustainable infection transmission for clusters to occur. At least some CMW communities in Qatar have reached or nearly reached herd immunity for SARS-CoV-2 infection at a proportion of ever infection of 65-70%.
Resveratrol And Pterostilbene Potently Inhibit SARS-CoV-2 Replication In Vitro
Authors: ter Ellen Bram M. , Kumar Nilima Dinesh , Bouma Ellen M. , Troost Berit , van de Pol Denise P.I. , van der Ende-Metselaar Heidi H. , Apperloo Leonie , van Gosliga Djoke , van den Berge Maarten , Nawijn Martijn C. , van der Voort Peter H.J. , Moser Jill , Rodenhuis-Zybert Izabela A. , Smit Jolanda M.
Published: September 2020

The current COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has an enormous impact on human health and economy. In search for therapeutic options, researchers have proposed resveratrol, a food supplement with known antiviral, anti-inflammatory and anti-oxidant properties as an advantageous antiviral therapy for SARS-CoV-2 infection. Here, we provide evidence that both resveratrol and its metabolically more stable structural analog, pterostilbene, exhibit potent antiviral properties against SARS-CoV-2in vitro. Resveratrol and pterostilbene showed antiviral activity in African green monkey kidney cells and in human primary bronchial epithelial cells cultured in an air-liquid interface system. Both compounds actively inhibit virus replication within infected cells as reduced virus progeny production was observed when the compound was added at post-inoculation conditions. Without replenishment of the compound, antiviral activity was observed up to roughly 5 rounds of replication, demonstrating the long-lasting effect of these compounds. Collectively, our data indicate that resveratrol and pterostilbene are promising antiviral compounds to treat SARS-CoV-2 infection. Because these results represent laboratory findings in cells, we advocate evaluation of these compounds in clinical trials before statements are made whether or not these drugs are advantageous for COVID-19 treatment.
ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins
Authors: Ayyappan Vinay , Wat Ricky , Barber Calvin , Vivelo Christina A. , Gauch Kathryn , Visanpattanasin Pat , Cook Garth , Sazeides Christos , Leung Anthony K. L.
Published: September 2020

ADP-ribosylation is a protein modification responsible for biological processes such as DNA repair, RNA regulation, cell cycle, and biomolecular condensate formation. Dysregulation of ADP-ribosylation is implicated in cancer, neurodegeneration, and viral infection. We developed ADPriboDB (adpribodb.leunglab.org) to facilitate studies in uncovering insights into the mechanisms and biological significance of ADP-ribosylation. ADPriboDB 2.0 serves as a one-stop repository comprising 48,346 entries and 9,097 ADP-ribosylated proteins, of which 6,708 were newly identified since the original database release. In this updated version, we provide information regarding the sites of ADP-ribosylation in 32,946 entries. The wealth of information allows us to interrogate existing databases or newly available data. For example, we found that ADP-ribosylated substrates are significantly associated with the recently identified human protein interaction networks associated with SARS-CoV-2, which encodes a conserved protein domain called macrodomain that binds and removes ADP-ribosylation. In addition, we create a new interactive tool to visualize the local context of ADP-ribosylation, such as structural and functional features as well as other post-translational modifications (e.g., phosphorylation, methylation and ubiquitination). This information provides opportunities to explore the biology of ADP-ribosylation and generate new hypotheses for experimental testing.
Transcriptome analysis of resistant and susceptible pepper (Capsicum annuumL.) in response toXanthomonas campestrispv.Vesicatoria
Authors: Gao Shenghua , Wang Fei , Niran Juntawong , Li Ning , Yin Yanxu , Yu Chuying , Jiao Chunhai , Yao Minghua
Published: September 2020

Bacterial spot (BS) disease of pepper, incited byXanthomonas campestrispv.Vesicatoria(Xcv), is one of the most serious diseases. For a comparative analysis of defense response toXcvinfection, we performed a transcriptome analysis of BS -susceptible cultivar ECW and -resistant cultivar VI037601 using the HiSeq™ 2500 sequencing platform. Approximately 140.15 G clean data were generated from eighteen libraries. From the libraries generated, we identified 52,041 genes including 35,336 reference genes, 16,705 novel transcripts, and 4,794 differentially expressed genes (DEGs). There were 1,291, 2,956, 1,795 and 2,448 DEGs in ECW-24h-vs-ECW-0h, ECW-48h-vs-ECW-0h, VI037601-24h-vs-VI037601-0h and VI037601-48h-vs-VI037601-0h groups, respectively. Interestingly, DEGs involved in disease response in the resistant variety were induced at an earlier stage and at higher levels compared with the susceptible variety. Key enriched categories included amino sugar and nucleotide sugar metabolism, sesquiterpenoid and triterpenoid biosynthesis and MAPK signaling pathway. Moreover, 273 DEGs only differentially expressed in VI037601 and 436 overlapping DEGs in ECW and VI037601 postXcvinoculation, including NBS-LRR genes, oxidoreductase gene, WRKY and NAC transcription factors were identified, which were mainly involved in metabolic process, response to stimulus and biological regulation pathways. Quantitative RT-PCR of sixteen selected DEGs further validated the RNA-seq differential gene expression analysis. Our results will provide a valuable resource for understanding the molecular mechanisms of pepper resistance toXcvinfection and improving pepper resistance cultivars againstXcv.
Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA
Authors: Bouvier Déborah , Ferrand Juliette , Chevallier Odile , Paulsen Michelle T. , Ljungman Mats , Polo Sophie E.
Published: September 2020

Transcription restart after a genotoxic challenge is a fundamental yet poorly understood process. Here, we dissect the interplay between transcription and chromatin restoration after DNA damage by focusing on the human histone chaperone complex HIRA, which is required for transcription recovery post UV. We demonstrate that HIRA is recruited to UV-damaged chromatin via the ubiquitin-dependent segregase VCP to deposit new H3.3 histones. However, this local activity of HIRA is dispensable for transcription recovery. Instead, we reveal a genome-wide function of HIRA in transcription restart that is independent of new H3.3 and not restricted to UV-damaged loci. HIRA coordinates with ASF1B to control transcription restart by two independent pathways: by stabilizing the associated subunit UBN2 and by reducing the expression of the transcription repressor ATF3. Thus, HIRA primes UV-damaged chromatin for transcription restart at least in part by relieving transcription inhibition rather than by depositing new H3.3 as an activating bookmark.
Recent advances in the development of high-resolution 3D cadmium–zinc–telluride drift strip detectors
Authors: Abbene Leonardo , Gerardi Gaetano , Principato Fabio , Buttacavoli Antonino , Altieri Saverio , Protti Nicoletta , Tomarchio Elio , Del Sordo Stefano , Auricchio Natalia , Bettelli Manuele , Amadè Nicola Sarzi , Zanettini Silvia , Zappettini Andrea , Caroli Ezio
Published: September 2020

In the last two decades, great efforts have been made in the development of 3D cadmium–zinc–telluride (CZT) detectors operating at room temperature for gamma-ray spectroscopic imaging. This work presents the spectroscopic performance of new high-resolution CZT drift strip detectors, recently developed at IMEM-CNR of Parma (Italy) in collaboration with due2lab (Italy). The detectors (19.4 mm × 19.4 mm × 6 mm) are organized into collecting anode strips (pitch of 1.6 mm) and drift strips (pitch of 0.4 mm) which are negatively biased to optimize electron charge collection. The cathode is divided into strips orthogonal to the anode strips with a pitch of 2 mm. Dedicated pulse processing analysis was performed on a wide range of collected and induced charge pulse shapes using custom 32-channel digital readout electronics. Excellent room-temperature energy resolution (1.3% FWHM at 662 keV) was achieved using the detectors without any spectral corrections. Further improvements (0.8% FWHM at 662 keV) were also obtained through a novel correction technique based on the analysis of collected-induced charge pulses from anode and drift strips. These activities are in the framework of two Italian research projects on the development of spectroscopic gamma-ray imagers (10–1000 keV) for astrophysical and medical applications.
Counting-loss correction method based on dual-exponential impulse shaping
Authors: Liu Yi , Wang Ming , Wan Wenjie , Zhou Jianbin , Hong Xu , Liu Fei , Yu Jie
Published: September 2020

Under the condition of high counting rate, the phenomenon of nuclear pulse signal pile-up using a single exponential impulse shaping method is still very serious, and leads to a severe loss in counting rate. A real nuclear pulse signal can be expressed as a dual-exponential decay function with a certain rising edge. This paper proposes a new dual-exponential impulse shaping method and shows its deployment in hardware to test its performance. The signal of a high-performance silicon drift detector under high counting rate in an X-ray fluorescence spectrometer is obtained. The result of the experiment shows that the new method can effectively shorten the dead-time caused by nuclear signal pile-up and correct the counting rate.
Crystal structures ofcatena-poly[[μ-aqua-diaqua(μ3-2-methylpropanoato-κ4O:O,O′:O′)calcium] 2-methylpropanoate dihydrate],catena-poly[[μ-aqua-diaqua(μ3-2-methylpropanoato-κ4O:O,O′:O′)strontium] 2-methylpropanoate dihydrate] andcatena-poly[[μ-aqua-diaqua(μ3-2-methylpropanoato-κ4O:O,O′:O′)(calcium/strontium)] 2-methylpropanoate dihydrate]
Authors: Samolová Erika , Fábry Jan
Published: September 2020

The crystal structures ofcatena-poly[[μ-aqua-diaqua(μ3-2-methylpropanoato-κ4O:O,O′:O′)calcium] 2-methylpropanoate dihydrate], {[Ca(C4H7O2)(H2O)3](C4H7O2)·2H2O}n, (I),catena-poly[[μ-aqua-diaqua(μ3-2-methylpropanoato-κ4O:O,O′:O′)strontium] 2-methylpropanoate dihydrate], {[Sr(C4H7O2)(H2O)3](C4H7O2)·2H2O}n, (II), andcatena-poly[[μ-aqua-diaqua(μ3-2-methylpropanoato-κ4O:O,O′:O′)(calcium/strontium)] 2-methylpropanoate dihydrate], {[(Ca,Sr)(C4H7O2)(H2O)3](C4H7O2)·2H2O}n, (III), are related. (III) can be considered as an Sr-containing solid solution of (I), with Ca2+and Sr2+occupationally disordered in the ratio 0.7936 (16):0.2064 (16). (I)/(III) and (II) are homeotypic with different space groups ofPbcaandCmce, respectively. All the title crystal structures are composed of hydrophilic sheets containing the cations, carboxylate groups as well as water molecules. The hydrophobic layers, which consist of 2-methylpropanoate chains, surround the hydrophilic sheets from both sides, thus forming a sandwich-like structure extending parallel to (001). The cohesion forces within these sheets are the cation–oxygen bonds and O—H...O hydrogen bonds of moderate strength. Stacking of these sandwiches along [001] is consolidated by van der Waals forces. The structures contain columns defined by the cation–oxygen interactions in which just one symmetry-independent 2-methylpropanoate anion is included, together with three water molecules. These molecules participate in an irregular coordination polyhedron composed of eight O atoms around the cation. Additional water molecules as well as the second 2-methylpropanoate anion are not part of the coordination sphere. These molecules are connected to the above-mentioned columns by O—H...O hydrogen bonds of moderate strength. In (II), the Sr2+cation, two of the coordinating water molecules and both anions are situated on a mirror plane with a concomitant positional disorder of the 2-methylpropyl groups; the non-coordinating water molecule also shows positional disorder of its hydrogen atom.
The N-terminal length and side-chain composition of CXCL13 affect crystallization, structure and functional activity
Authors: Rosenberg Eric M. , Herrington James , Rajasekaran Deepa , Murphy James W. , Pantouris Georgios , Lolis Elias J.
Published: September 2020

CXCL13 is the cognate chemokine agonist of CXCR5, a class A G-protein-coupled receptor (GPCR) that is essential for proper humoral immune responses. Using a `methionine scanning' mutagenesis method on the N-terminus of CXCL13, which is the chemokine signaling region, it was shown that minor length alterations and side-chain substitutions still result in CXCR5 activation. This observation indicates that the orthosteric pocket of CXCR5 can tolerate these changes without severely affecting the activity. The introduction of bulk on the ligand was well tolerated by the receptor, whereas a loss of contacts was less tolerated. Furthermore, two crystal structures of CXCL13 mutants were solved, both of which represent the first uncomplexed structures of the human protein. These structures were stabilized by unique interactions formed by the N-termini of the ligands, indicating that CXCL13 exhibits substantial N-terminal flexibility while the chemokine core domain remains largely unchanged. Additionally, it was observed that CXCL13 harbors a large degree of flexibility in the C-terminal extension of the ligand. Comparisons with other published structures of human and murine CXCL13 validate the relative rigidity of the core domain as well as the N- and C-terminal mobilities. Collectively, these mutants and their structures provide the field with additional insights into how CXCL13 interacts with CXCR5.
10-Phenyl-10H-phenoxazine-4,6-diol tetrahydrofuran monosolvate
Authors: Whalen Aislinn C. , Hernandez Brito Claudia , Choi Kyoung H. , Warner Ellen J. T. , Thole David A. , Gau Michael R. , Carroll Patrick J. , Anstey Mitchell R.
Published: September 2020

In the crystalline state of the title solvate, C18H13NO3·C4H8O, hydrogen-bonding interactions between hydroxyl groups on a phenoxazine backbone and the tetrahydrofuran solvent are observed that suggest the ability for this compound to act as a chelating ligand. The O...O donor–acceptor distances for this hydrogen bonding are 2.7729 (15) and 2.7447 (15) Å. The three-ring backbone of the phenoxazine bends out of planarity by 18.92 (3)°, as computed using mean planes that encompass each half of the three-ring structure, with the central N and O atoms forming the line of flexion. In the crystal, a π–π stacking arrangement exists between inversion-related molecules, with a centroid-to-centroid distance of 3.6355 (11) Å. In the disordered tetrahydrofuran solvate, all atoms except oxygen were modeled over two positions, with occupancies of 0.511 (8) and 0.489 (8).
2,2-Bis[3,5-bis(dimethylamino)phenyl]-1,1,1,3,3,3-hexamethyltrisilane
Authors: Mizuhata Yoshiyuki , Iwai Kento , Tokitoh Norihiro
Published: September 2020

The title compound, C26H48N4Si3, was synthesized by the reaction of 2,2-dichlorotrisilane with 3,5-bis(dimethylamino)phenyllithium. In the molecule, the dihedral angle between the benzene rings is 57.57 (7)° and the Si—Si—Si bond angle is 110.08 (2)°. In the crystal, molecules are linked via an SiC–H...π(aryl) interaction, forming a chain along the c-axis direction.
“You make me miss Pune so much”: memory making and documenting in a Virtual Zenana
Authors: Kizhakkethil Priya
Published: September 2020

Purpose

The purpose of the study is to look at memory making and the documenting of memories, as a part of the document and information experience of women belonging to the Indian diaspora in a leisure context.

Design/methodology/approach

A qualitative research approach was inspired by institutional ethnography, and data are collected through semi-structured interviews and by collecting comments posted on five fan fiction blogs.

Findings

Early observations show that memory making and documenting of those memories is a part of the document experience of the research participants. It also points to the role of social interactions in that experience as well as the recording of one's document experience in the making or deriving of document meaning.

Originality/value

This study aims to contribute toward conceptual growth in the area of information and document experience. It also aims to address a gap in the literature that looks at cultural memory evocation and how it is documented, as well as looking at the interplay between affordances of new media, memory making and documentary practices especially with respect to virtual communities. And when looked at through the prism of migration and leisure, it can be even more interesting.
Systematically reviewing servant leadership
Authors: Mcquade Katie Elizabeth , Harrison Christian , Tarbert Heather
Published: September 2020

Purpose

The purpose of this paper is to provide a comprehensive overview of the literature concerning servant leadership. The paper identifies the existing themes present within the servant leadership literature. This allows it to determine where the research concerning servant leadership lies at present and make recommendations as to further potential areas for research. It further identifies the skills necessary for servant leadership.

Design/methodology/approach

The paper follows a rigorous three-step systematic literature review (SLR) process to identify the relevant evidence to answer the research questions. The paper disseminates the results and presents them by way of a descriptive analysis. It also conducts a thematic analysis to further determine answers to the research questions.

Findings

The paper found that the most prominent themes in the servant leadership literature are values, literature reviews, behaviour, assessments, performance, characteristics and antecedents. Additionally, the paper finds that the skills necessary for servant leadership are empathy, listening, communication and trust. The review also identified gaps in the research both methodologically and empirically. It showed that more qualitative research is needed with regard to servant leadership. Furthermore, the development of empirically tested frameworks is necessary within the phenomenon.

Originality/value

Servant leadership is a phenomenon which is lacking in a reliable, validated SLR, which this paper presents. Additionally the originality of this paper lies in its recommendations for further research which are based upon the findings of a thematic analysis. As of yet, such recommendations have not yet been made within the field of servant leadership.
Unsteady stagnation-point flow and heat transfer of fractional Maxwell fluid towards a time dependent stretching plate with generalized Fourier’s law
Authors: Bai Yu , Huo Lamei , Zhang Yan
Published: September 2020

Purpose

The purpose of this study is to investigate the unsteady stagnation-point flow and heat transfer of fractional Maxwell fluid towards a time power-law-dependent stretching plate. Based on the characteristics of pressure in the boundary layer, the momentum equation with the fractional Maxwell model is firstly formulated to analyze unsteady stagnation-point flow. Furthermore, generalized Fourier’s law is considered in the energy equation and boundary condition of convective heat transfer.

Design/methodology/approach

The nonlinear fractional differential equations are solved by the newly developed finite difference scheme combined with L1-algorithm, whose convergence is verified by constructing a numerical example.

Findings

Some interesting results can be revealed. The larger fractional derivative parameter of velocity promotes the flow, while the smaller fractional derivative parameter of temperature accelerates the heat transfer. The temperature boundary layer is thicker than the velocity boundary layer, and the velocity enlarges as the stagnation parameter raises. This is because when Prandtl number < 1, the capacity of heat diffusion is greater than that of momentum diffusion. It is to be observed that all the temperature profiles first enhance a little and then reduce rapidly, which indicates the thermal retardation of Maxwell fluid.

Originality/value

The unsteady stagnation-point flow model of Maxwell fluid is extended from integral derivative to fractional derivative, which has more flexibility to describe viscoelastic fluid’s complex dynamic process and provide a theoretical basis for industrial processing.