bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of Separate Foreign Proteins from the Rotavirus NSP3 Genome Segment Using a Translational 2A Stop-Restart Element
Authors: Philip Asha A. , Patton John T.
Published: May 2020

The segmented 18.5-kB dsRNA genome of rotavirus expresses 6 structural and 6 nonstructural proteins. We investigated the possibility of using the recently-developed plasmid-based rotavirus reverse genetics (RG) system to generate recombinant viruses that express a separate foreign protein, in addition to the 12 viral proteins. To address this, we replaced the NSP3 open-reading-frame (ORF) of the segment 7 (pT7/NSP3) transcription vector used in the RG system with an ORF encoding NSP3 fused to a fluorescent reporter protein (i.e., UnaG, mRuby, mKate, or TagBFP). Inserted at the fusion junction was a teschovirus 2A-like self-cleaving element designed to direct the separate expression of NSP3 and the fluorescent protein. Recombinant rotaviruses made with the modified pT7/NSP3 vectors were well growing, generally genetically stable, and expressed NSP3 and a separate fluorescent protein detectable by live cell imaging. NSP3 made by the recombinant viruses was functional, inducing nuclear accumulation of cellular poly(A)-binding protein. Further modification of the NSP3 ORF showed that it was possible to generate recombinant viruses encoding 2 foreign proteins (mRuby and UnaG) in addition to NSP3. Our results demonstrate that, through modification of segment 7, the rotavirus genome can be increased in size to at least 19.8 kB and can be used to produce recombinant rotaviruses expressing a full complement of viral proteins and multiple foreign proteins. The generation of recombinant rotaviruses expressing fluorescent proteins will be valuable for the study of rotavirus replication and pathogenesis by live cell imagining and suggest that rotaviruses may prove useful as expression vectors.

Importance

Rotaviruses are a major cause of severe gastroenteritis in infants and young children. Recently, a highly efficient reverse genetics system was developed that allows genetic manipulation of the rotavirus segmented double-stranded RNA genome. Using the reverse genetics system, we show that it is possible to modify one of the rotavirus genome segments (segment 7) such that virus gains the capacity to express a separate foreign protein, in addition to the full complement of viral proteins. Through this approach, we have generated wildtype-like rotaviruses that express various fluorescent reporter proteins, including UnaG (green), mRuby (far red), mKate (red), and TagBFP (blue). Such strains will be of value in probing rotavirus biology and pathogenesis by live-cell imagining techniques. Notably, our work indicates that the rotavirus genome is remarkably flexible and able to accommodate significant amounts of foreign RNA sequence, raising the possibility of using the virus as vaccine expression vector.
Repurposing Ribo-Seq to provide insights into structured RNAs
Authors: Fremin Brayon J. , Bhatt Ami S.
Published: May 2020

Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, this method can enrich RNAs that are not bound by ribosomes, but rather, are protected from degradation in another way. For example, Escherichia coli Ribo-Seq libraries also capture reads from most non-coding RNAs (ncRNAs). These fragments of ncRNAs pass all size selection steps of the Ribo-Seq protocol and survive hours of MNase treatment, presumably without protection from the ribosome or other macromolecules or proteins. Since bacterial ribosome profiling does not directly isolate ribosomes, but instead uses broad size range cutoffs to fractionate actively translated RNAs, it is understandable that some ncRNAs are retained after size selection. However, how these ‘contaminants’ survive MNase treatment is unclear. Through analyzing metaRibo-Seq reads across ssrS, a well established structured RNA in E. coli, and structured direct repeats from Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays in Ruminococcus lactaris, we observed that these RNAs are protected from MNase treatment by virtue of their secondary structure. Therefore, large volumes of data previously discarded as contaminants in bacterial Ribo-Seq experiments can, in fact, be used to gain information regarding the in vivo secondary structure of ncRNAs, providing unique insight into their native functional structures.

Importance

We observe that ‘contaminant’ signals in bacterial Ribo-Seq experiments that are often disregarded and discarded, in fact, strongly overlap with structured regions of ncRNAs. Structured ncRNAs are pivotal mediators of bioregulation in bacteria and their functions are often reliant on their specific structures. We present an approach to access important RNA structural information through merely repurposing ‘contaminant’ signals in bacterial Ribo-Seq experiments. This powerful approach enables us to partially resolve RNA structures, identify novel structured RNAs, and elucidate RNA structure-function relationships in bacteria at a large-scale and in vivo.
Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience
Authors: Olalla Julian , Correa Ana M , Martin-Escalante Maria Dolores , Hortas Maria Luisa , Martin-Sendarrubias Maria Jesus , Fuentes Victor , Sena Gabriel , Garcia-Alegria Javier ,   ROBLE Group
Published: May 2020

Objective: determine the percentage of healthcare workers (HCW) carrying SARS-CoV-2 in high exposure areas of the hospital.
Design: cross- sectional study during April 15-24th in Hospital Costa del Sol (Marbella, Spain), excluding HCW with previous COVID19.
Setting: hospital based, focused on patient care areas COVID19.
Participants: 498 subjects, 80% women. Participation was offered to all the HCW of Emergencies, Intensive Care and Anesthesia, Internal Medicine and Pneumology. Other units not directly involved in the care of these patients were offered to participate.
Intervention: naso and oropharyngeal PCR determination was performed together with IgG and IgM antibody determination by immunochromatography. On the day of sampling, a health questionnaire was answered, reporting symptoms on the same day and in the previous fourteen days.
Main outcome measures: percentage of HCW with positive PCR for SARS-CoV-2, percentage of HCW with positive IgG for SARS-CoV-2.
Results: Two individuals were detected with PCR for SARS-CoV-2 positive (0.4%). Both were asymptomatic on the day of sampling, but one of them had had a CoVID-19 compatible picture in the previous two weeks and had positive IgG and IgM; therefore, only one subject was truly asymptomatic carrier (0.2%). 9 workers with positive IgG (1.8%) were detected.
Conclusions: the prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This type of strategy can be one more tool in controlling the pandemic.
Combined effect of biological and physical stress on artificial production of agarwood oleoresin inAquilaria malaccensis
Authors: Chhipa Hemraj , Kaushik Nutan
Published: May 2020

Agarwood is the most expensive wood of the world and highly demanded wood in perfumery industry and ritual ceremonies of various religions. Agarwood is the infectious wood part ofAquilariatree. Naturally, production of agarwood inAquilariatakes 10-20 years of time and it can develop only in 1-2% ofAquilariatrees. Different types of biological, chemical and physical methods have been developed for artificial production of agarwood to fulfil the rising demand of the market. In the current article, we tried to explore combined effect of physical and biological stress in the form of stick method to improve agarwood production inAquilaria malaccensisand compared it with well-known artificial fungal infection syringe method. Total 21 fungal strains were applied alone (syringe method) and with bamboo sticks (stick method). We found maximum infection occurred in stick method by fungiPenicillium polonicumAQGGR1.1 with 10 cm infection length. Artificial induction of marker compounds of agarwood, benzyl acetone and anisyl acetone were measured mostly in stick method, induced by 71.4% fungal strains grown on bamboo sticks, while alone only 42.9% fungi can induced in syringe method.Penicillium aethiopicumAQGGR1.2 found highly agarwood oleoresin inducing fungus in stick method and shown high potential agent in stick method for artificial production of agarwood.
Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection
Authors: Wan Jinkai , Xing Shenghui , Ding Longfei , Wang Yongheng , Zhu Dandan , Rong Bowen , Wang Siqing , Chen Kun , He Chenxi , Yuan Songhua , Qiu Chengli , Zhao Chen , Zhang Xiaoyan , Wang Xiangxi , Lu Yanan , Xu Jianqing , Lan Fei
Published: May 2020

The coronavirus induced disease 19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a worldwide threat to human lives, and neutralizing antibodies present a great therapeutic potential in curing affected patients. We purified more than one thousand memory B cells specific to SARS-CoV-2 S1 or RBD (receptor binding domain) antigens from 11 convalescent COVID-19 patients, and a total of 729 naturally paired heavy and light chain fragments were obtained by single B cell cloning technology. Among these, 178 recombinant monoclonal antibodies were tested positive for antigen binding, and the top 13 binders with Kdbelow 0.5 nM are all RBD binders. Importantly, all these 13 antibodies could block pseudoviral entry into HEK293T cells overexpressing ACE2, with the best ones showing IC50s around 2-3 nM. We further identified 8 neutralizing antibodies against authentic virus with IC50s within 10 nM. Among these, 414-1 blocked authentic viral entry at IC50 of 1.75 nM and in combination with 105-38 could achieve IC50 as low as 0.45 nM. Meanwhile, we also found that 3 antibodies could cross-react with the SARS-CoV spike protein. Altogether, our study provided a panel of potent human neutralizing antibodies for COVID19 as therapeutics candidates for further development.
In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy
Authors: Uwizeye Clarisse , Decelle Johan , Jouneau Pierre-Henri , Gallet Benoit , Keck Jean-Baptiste , Moriscot Christine , Chevalier Fabien , Schieber Nicole L. , Templin Rachel , Curien Gilles , Schwab Yannick , Schoehn Guy , Zeeman Samuel C. , Falconet Denis , Finazzi Giovanni
Published: May 2020

Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management:i)conserved cell-volume fractions occupied by the different organelles;ii)consistent plastid-mitochondria interactions,iii)constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.
Local RNA translation controls cell migration and Rab GTPase function
Authors: Moissoglu Konstadinos , Stueland Michael , Gasparski Alexander N. , Wang Tianhong , Jenkins Lisa M. , Hastings Michelle L. , Mili Stavroula
Published: May 2020

Numerous RNAs exhibit specific distribution patterns in mammalian cells. However, the functional and mechanistic consequences are relatively unknown. We investigate here the functional role of RNA localization at cellular protrusions of mesenchymal migrating cells, using as a model theRAB13RNA, which encodes a GTPase important for vesicle-mediated membrane trafficking. WhileRAB13RNA is enriched at peripheral protrusions, the expressed protein is concentrated perinuclearly. By specifically preventingRAB13RNA localization, we show that peripheralRAB13translation is not important for the overall distribution of the RAB13 protein, or its ability to associate with membranes, but is required for full activation of the GTPase and for efficient cell migration. This effect is mediated by a co-translational association of RAB13 with the exchange factor RABIF. Our results indicate that RAB13-RABIF association at the periphery is required for directing RAB13 GTPase activity to promote cell migration. Thus, translation of RAB13 in specific subcellular environments imparts the protein with distinct properties and highlights a means of controlling protein function through local RNA translation.
Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products
Authors: Kloosterman Alexander M. , Cimermancic Peter , Elsayed Somayah S. , Du Chao , Hadjithomas Michalis , Donia Mohamed S. , Fischbach Michael A. , van Wezel Gilles P. , Medema Marnix H.
Published: May 2020

Most clinical drugs are based on microbial natural products, with compound classes including polyketides (PKS), non-ribosomal peptides (NRPS), fluoroquinones and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295Streptomycesgenomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a novel subfamily of lanthipeptides, designated Class V. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria.

Code and data availability

The source code of DecRiPPter is freely available online athttps://github.com/Alexamk/decRiPPter. Results of the data analysis are available online athttp://www.bioinformatics.nl/~medem005/decRiPPter_strict/index.htmlandhttp://www.bioinformatics.nl/~medem005/decRiPPter_mild/index.html(for the strict and mild filters, respectively). All training data and code used to generate these, as well as outputs of the data analyses, are available on Zenodo atdoi:10.5281/zenodo.3834818.
Dynamic proteomics profiling ofLegionella pneumophilainfection unveils modulation of the host mitochondrial stress response pathway
Authors: Noack Julia , Jimenez-Morales David , Stevenson Erica , Moss Tom , Jang Gwendolyn , Krogan Nevan J. , Swaney Danielle L. , Mukherjee Shaeri
Published: May 2020

The human pathogenLegionella pneumophila (L.p.)secretes ~330 bacterial effector proteins into the host cell which interfere with numerous cellular pathways and often regulate host cell proteins through post-translational modifications. However, the cellular targets and functions of mostL.p.effectors are not known. In order to obtain a global overview of potential targets of these effectors, we analyzed the host cell proteome, ubiquitinome, and phosphoproteome duringL.p.infection. Our analysis reveals dramatic spatiotemporal changes in the host cell proteome that are dependent on the secretion of bacterial effectors. Strikingly, we show thatL.p.substantially reshapes the mitochondrial proteome and modulates mitochondrial stress response pathways such as the mitochondrial unfolded protein response (UPRmt). To our knowledge, this is the first evidence of manipulation of the UPRmtby a bacterial pathogen in mammalian cells. In addition, we have identified a previously uncharacterizedL.p.effector that is targeted to host cell mitochondria and protects mitochondrial network integrity during mitochondrial stress.
Numerical solution of fractional Bratu–type BVPs: a generalized variational iteration approach
Authors: Assadi Reem , Khuri Suheil , Louhichi Issam
Published: May 2020

Purpose

The purpose of this study is to implement a newly introduced numerical scheme for the numerical solution of a class of nonlinear fractional Bratu-type boundary value problems (BVPs).

Design/methodology/approach

This strategy is based on a generalization of the variational iteration method (VIM). This proposed generalized VIM (GVIM) is particularly suitable for tackling BVPs.

Findings

This scheme yields accurate solutions for a class of nonlinear fractional Bratu-type BVPs, for which the errors are uniformly distributed across a given domain. A proof of convergence is included. The numerical results confirm that this approach overcomes the deficiency of the VIM and other methods that exist in the literature in the sense that the solution does not deteriorate as the authors move away from the initial starting point.

Originality/value

The method introduced is based on original research that produces new knowledge. To the best of the authors’ knowledge, this is the first time that this GVIM is applied to fractional BVPs.
A breakfast of champions: brand marketing lessons from the Great Depression
Authors: Hirsch Peter Buell
Published: May 2020

Purpose

This paper aims to examine whether the behavior of brands during the Great Depression held lessons for the aftermath of the coronavirus pandemic.

Design/methodology/approach

A review of brand marketing and advertising from the 1920s and 1930s.

Findings

There are many learnings from the Great Depression that are instructive for today’s brand marketers dealing with COVID-19.

Research limitations/implications

The review of the literature is not comprehensive and the findings are subjective.

Practical implications

Today’s brands can learn a great deal from the 1930s such as to take advantage of opportunities and avoid mistakes in today’s difficult environment.

Social implications

By handling today’s challenges skillfully, brands can refresh relationships with consumers overwhelmed with choices.

Originality/value

Though there was some commentary on this subject following the Great Recession of 2009, there has been little written about the lessons in brand marketing in the current situation.
Assessment of heavy metals by ICP‐OES and their impact on insulin stimulating hormone and carbohydrate metabolizing enzymes
Authors: Saba Shakil , Akash Muhammad Sajid Hamid , Rehman Kanwal , Saleem Uzma , Fiayyaz Fareeha , Ahmad Tanvir
Published: May 2020

Arsenic (As) and cadmium (Cd) have recently emerged as major health concerns owing to their strong association with diabetes mellitus (DM). We aimed to investigate the heavy metals exposure towards incidence of DM at various enzymatic and hormonal levels. Additionally, association of As and Cd with Zinc (Zn, essential metal) was also evaluated. Spot urine samples were collected to assess As, Cd and Zn through ICP‐OES. Serum was analyzed by assay method for fasting blood glucose, liver and renal function biomarkers. ELISA was performed to investigate the impact of heavy metals on HbA1c, α‐amylase, DPP‐IV, IGF‐1, leptin, GSH, MDA, SOD, HDL, FFA, TG and interleukin (IL)‐6. Association of heavy metals with DM was measured by odds ratio (OR) and level of significance was assessed by Chi‐squared test. Unpaired student's t‐test was used to compare DM‐associated risk factors in heavy metals‐exposed and unexposed participants. As and Cd were detectable in 75.4% and 83% participants with mean concentration of 75.5 ppb and 54.5 ppb, respectively. For As exposure, OR in the third quartile was maximum ie 1.34 (95% CI, 0.80 to 2.23), however the result was not statistically significant (P > .05). For Cd exposure, OR in the fourth quartile was considerably high, 1.62 (95% CI, 1.00 to 2.61), with a significant probability value (P < .05). Urinary Cd was negatively associated with Zn. As and Cd exposure increases the incidence of DM in the general population. Impaired hormonal and enzymatic levels in diabetic and non‐diabetic exposed participants reflect the multiple organ damage by heavy metal exposure.
Directors of emergency medicine's beliefs about, barriers to, and enablers of solutions to emergency department crowding and access block
Authors: Rixon Andrew , Wilson Samuel , Judkins Simon , White Peter
Published: May 2020

Objective

To identify opportunities for directors of emergency medicine (DEMs) to lead change efforts to address ED crowding and access block.

Methods

DEMs were surveyed about their beliefs about, barriers to, and enablers of solutions to ED crowding and access block.

Results

Key barriers were insufficient resources, entrenched hospital culture, and lack of political will to address ED crowding and access block. Key enablers were developing hospital‐wide understanding of the problems, developing a supportive hospital culture, and improved engagement by hospital executive.

Conclusion

Addressing the political and cultural forces that sustain ED crowding and access block are key adaptive challenges requiring DEM leadership.
Factors affecting the accuracy of endoscopic ultrasound‐guided fine needle aspiration for the diagnosis of small (≤20 mm) pancreatic lesions
Authors: Li Hong Zhen , Peng Chun Yan , Shen Shan Shan , Wang Lei , Zhang Song , Xu Gui Fang , Kong Bo , Friess Helmut , Zou Xiao Ping , Lv Ying
Published: May 2020

Objective

To explore the diagnostic value of endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA) for small, solid or semi‐solid pancreatic lesions (≤20 mm) and the factors affecting its accuracy.

Methods

Altogether 92 patients with small, solid or semi‐solid pancreatic lesions who underwent EUS‐FNA at the Nanjing Drum Tower Hospital from November 2009 to January 2019 were retrospectively analyzed. Univariate and multivariate analyses were used to determine the factors affecting the accuracy of EUS‐FNA for detecting these lesions.

Results

Among the 92 cases, 56 (60.9%) were diagnosed as having malignant lesions and 36 (39.1%) as benign lesions, respectively. The overall sensitivity, specificity and accuracy of EUS‐FNA for the diagnosis of small, solid or semi‐solid pancreatic lesions were 71.4%, 100% and 82.6%, respectively. When considering the impact of the presence of a tissue core on the diagnosis, the sensitivity, specificity, and accuracy of EUS‐FNA with tissue core compared with those based on cytology alone were 77.3% vs 50.0%; 100% vs 100%; and 86.8% vs 62.5%, respectively. The multivariate analysis showed that larger tumor size (>15‐20 mm) (odds ratio [OR] 4.200, 95% confidence interval [CI] 1.21‐14.53, P = 0.023) and histologic diagnosis based on tissue core (OR 4.593, 95% CI 1.03‐20.47, P = 0.046) were related to a higher accuracy of EUS‐FNA. Adverse events were observed in three patients, all were treated conservatively and recovered within 3 days.

Conclusions

EUS‐FNA is effective and safe for diagnosing small pancreatic lesions. Tumor size and presence of tissue core are related to higher accuracy of the EUS‐FNA.
Assessment of the efficiency of different control programs to reduce Trioza apicalis Först. (Triozidae: Hemiptera) feeding damage and the spread of “Candidatus Liberibacter solanacearum” on carrots (Daucus carota ssp. sativus L.)
Authors: Nissinen Anne I. , Pihlava Juha‐Matti , Latvala Satu , Jauhiainen Lauri
Published: May 2020

The control of carrot psyllid Trioza apicalis Förster largely relies on chemical measures, and the current integrated pest management (IPM) strategy is based on pest scouting. The number of active ingredients available for psyllid control will further decline in the coming years. The need for alternative control measures is therefore urgent. In this work the efficiency of different control programs including a kaolin particle film and plant‐derived, crude saponin extract, chemical control, insect net and IPM (kaolin in combination with insecticides) programs to reduce psyllid feeding damage, reproduction and the spread of “Candidatus Liberibacter solanacearum” (CLso) in carrots was studied. Each year in 2016–2018, four replicates of each treatment were randomised in a row‐column design on a commercial carrot farm. After the treatments were executed, the psyllid nymphs and eggs were counted. At the harvest, the carrot roots and shoots were weighed, damages assessed, and samples were taken for CLso detection from 50 plants at each replicate. Kaolin treatment alone and in combination with insecticides effectively reduced the number of psyllid nymphs and eggs in all the years studied. Saponin was applied only on the first year, since it significantly increased the number of T. apicalis eggs compared to other treatments. The insect net was superior to other treatments in all the studied aspects in all the years. Under normal weather conditions, the highest root weight was harvested under the insect net, followed by the chemical control program consisting of pyrethroids, kaolin treatment, untreated control and saponin treatment. During extreme weather conditions, chemical control programs were not effective at protecting the carrots from psyllid feeding, which was reflected as low root yield. In all years, the carrot leaf damage percent negatively correlated with the root weight. Similarly, the shoot:root ratio increased as the leaf‐curling percentage rose, which was even pronounced under drought stress. The effect of climatic stress should be considered when developing IPM strategies.
Neuronal control of lipid metabolism by STR‐2 G protein‐coupled receptor promotes longevity in Caenorhabditis elegans
Authors: Dixit Anubhuti , Sandhu Anjali , Modi Souvik , Shashikanth Meghana , Koushika Sandhya P. , Watts Jennifer L. , Singh Varsha
Published: May 2020

The G protein‐coupled receptor (GPCR) encoding family of genes constitutes more than 6% of genes in Caenorhabditis elegans genome. GPCRs control behavior, innate immunity, chemotaxis, and food search behavior. Here, we show that C. elegans longevity is regulated by a chemosensory GPCR STR‐2, expressed in AWC and ASI amphid sensory neurons. STR‐2 function is required at temperatures of 20°C and higher on standard Escherichia coli OP50 diet. Under these conditions, this neuronal receptor also controls health span parameters and lipid droplet (LD) homeostasis in the intestine. We show that STR‐2 regulates expression of delta‐9 desaturases, fat‐5, fat‐6 and fat‐7, and of diacylglycerol acyltransferase dgat‐2. Rescue of the STR‐2 function in either AWC and ASI, or ASI sensory neurons alone, restores expression of fat‐5, dgat‐2 and restores LD stores and longevity. Rescue of stored fat levels of GPCR mutant animals to wild‐type levels, with low concentration of glucose, rescues its lifespan phenotype. In all, we show that neuronal STR‐2 GPCR facilitates control of neutral lipid levels and longevity in C. elegans.
The effects of morphine withdrawal and conditioned withdrawal on memory consolidation and c‐Fos expression in the central amygdala
Authors: Baidoo Nana , Wolter Michael , Holahan Matthew R. , Teale Tanisse , Winters Boyer , Leri Francesco
Published: May 2020

The current study tested the hypothesis that drug withdrawal contributes to the addiction cycle in part because of an action on memory consolidation. Hence, four experiments in male Sprague–Dawley rats compared the effects of precipitated morphine withdrawal and conditioned morphine withdrawal on the consolidation of object memory and on activation of c‐Fos in the central nucleus of the amygdala (CeA). It was found that immediate, but not 6 h delayed, post sample administration of 3 mg/kg of naltrexone significantly enhanced object memory in rats maintained, or previously maintained, on 10 mg/kg/day of morphine via osmotic minipumps. To establish whether conditioned withdrawal could also alter object memory, a contextual conditioning procedure was employed whereby morphine‐maintained (10 mg/kg/day) animals received naltrexone (3 mg/kg) in a distinctive context (CS+) and vehicle in a separate context (CS−) for 10 days. During conditioning in the CS+, naltrexone suppressed locomotor activity, caused a rapid body weight loss and increased frequency of wet dog shakes. Interestingly, confinement to this CS+ immediately, but not 6 h, after the sample phase, also enhanced object memory. Finally, posttraining naltrexone and exposure to the CS+ both induced significant expression of c‐Fos in the CeA. Therefore, this study reports for the first time that both acute precipitated withdrawal and conditioned withdrawal can facilitate memory consolidation, possibly through a common neural pathway that involves the central amygdala.
Bank Liquidity Creation, Regulations, and Credit Risk
Authors: Hsieh Meng‐Fen , Lee Chien‐Chiang
Published: May 2020

This study employs bank‐level data covering 3007 individual banks (commercial, savings, and others) in 27 Asian countries to investigate the determinants of bank liquidity creation, considering four conditional factors over the period 1999–2013: credit risk, deposit insurance, financial market regulations, and bank reforms. Bank liquidity creation is shown to be statistically and economically significantly positively related to real economic output, as well as illiquid assets and core deposits. Larger banks increase their liquid assets ratio, but decrease their credit commitment. Countries implementing an explicit deposit insurance scheme may lead to moral hazard and excessive bank risk taking. If supervisory authorities can force a bank to change its internal organizational structure, or have more power to take legal action against external auditors for negligence, or increase capital requirements, then banks generally reduce their lending activities. Nevertheless, larger banks are able to increase liquid assets and lending to those countries with stricter financial regulations.
Myeloid‐derived suppressor cells in obstetrical and gynecological diseases
Authors: Zheng Zi‐Meng , Yang Hui‐Li , Lai Zhen‐Zhen , Wang Cheng‐Jie , Yang Shao‐Liang , Li Ming‐Qing , Shao Jun
Published: May 2020

Myeloid‐derived suppressor cells (MDSCs) are a heterogeneous group of myeloid‐origin cells which have immunosuppressive activities in several conditions, such as cancer and inflammation. Recent research has also associated MDSCs with numerous obstetrical and gynecological diseases. During pregnancy, MDSCs accumulate to ensure maternal‐fetal immune tolerance, whereas they are decreased in patients who suffer from early miscarriage or pre‐eclampsia. While the etiology of endometriosis is still unknown, abnormal accumulation of MDSCs in the peripheral blood and peritoneal fluid, alongside an increased level of reactive oxygen species (ROS), has been observed in these patients, which is central to the cellular immune regulations by MDSCs. Additionally, the regulation of MDSCs observed in tumours is also applicable to gynecologic neoplasms, including ovarian cancer and cervical cancer. More recently, emerging evidence has shown that there are high levels of MDSCs in premature ovarian failure (POF) and in vitro fertilization (IVF), but the underlying mechanisms are unknown. In this review, the generation and mechanisms of MDSCs are summarized. In particular, the modulation of these cells in immune‐related obstetrical and gynecological diseases is discussed, including potential treatment options targeting MDSCs.
C‐reactive protein may rise after closed‐suction drainage removal in patients undergoing revision arthroplasty: a retrospective study
Authors: Xu Chi , Sun Yun‐Ming , Chai Wei , Chen Ji‐Ying
Published: May 2020

Background

Serum C‐reactive protein (CRP) has been one of the most commonly used markers to rule out early post‐operative infection following total joint arthroplasty. The phenomenon that CRP values rise after prolonged drainage removal may occur in clinical settings. The purpose of this study is to investigate (i) the prevalence and risk factors of such a phenomenon and (ii) whether the raised CRP is associated with post‐operative infection.

Methods

A retrospective review of 72 revision arthroplasties of the knee and hip with prolonged drainage from 2011 to 2016 was conducted. Perioperative CRP levels were obtained, and patients were divided into two groups according to whether CRP levels were elevated after drainage removal (raised CRP group and control group). Multivariate logistic regression analyses were performed to identify risk factors of raised CRP after drainage removal. The incidence of post‐operative wound complications and infection was compared between groups.

Results

Overall, the prevalence of raised CRP after drainage removal was 29.17% (21/72). CRP level before drainage removal was associated with the occurrence of such a phenomenon (adjusted odds ratio per 10‐mg/L increase 0.92, 95% confidence interval 0.87–0.97). The raised CRP levels decrease again within 3 days after drainage removal. There was no significant difference in the incidence of wound complications and infection between the raised CRP group and control group.

Conclusion

Almost one in three patients have raised CRP values after prolonged drainage removal following revision arthroplasty. However, CRP values can decrease again within 3 days after drainage removal without specific management.

Almost one in three patients have raised C‐reactive protein values after prolonged drainage removal following revision arthroplasty. However, C‐reactive protein values can decrease again within 3 days after drainage removal without specific management. Surgeons should remember that such a phenomenon may be not be a proxy for post‐operative infection following revision arthroplasty.
Development of the ‘People–Processes–Paradigm’ critical analysis tool for mortality and morbidity reviews: improving understanding of systems factors
Authors: Salindera Shehnarz , Brennan Meagan
Published: May 2020

Background

The impact of systems problems and human factors on delivering safe, high‐quality patient care is well recognized. In the surgical setting, mortality and morbidity reviews (MMRs) are the key forum for reviewing and analysing adverse events in patient care yet there is a paucity of simple tools for undertaking such analyses. The aim of this study was to develop and pilot a new tool for analysing mortality and morbidity cases incorporating human factors and systems analysis.

Methods

The published literature, professional standards, guidelines and existing audit tools for MMRs were reviewed. The ‘People–Processes–Paradigm’ tool was developed and pilot testing was undertaken and stakeholder feedback was obtained.

Results

Models found for undertaking systems‐based analysis of adverse surgical events included the 3D model, SEIPS and the Queensland Health human error and patient safety (HEAPS) Incident Management Tool. Guidelines for standards in MMRs are provided by the Royal Australasian College of Surgeons, New South Wales Clinical Excellence Commission and Australia and New Zealand audit of surgical mortality (ANZASM). The People–Processes–Paradigm model incorporates these standards and evidence‐based systems analysis tools into a single effective tool. The pilot study evaluating the use of this tool demonstrated it to be practical and easily applicable to regular use by clinicians, with the ability to be tailored to individual health service use. Improvements such as electronic format and clarification of case selection processes were recommended by users.

Conclusion

The People–Processes–Paradigm tool has been developed for surgeons by surgeons incorporating current professional, legal and regulatory requirements in Australasia, easily transferrable to electronic platforms. This model requires further testing for validation.
Relative contribution of ancient woodland indicator and non‐indicator species to herb layer distinctiveness in ancient semi‐natural, ancient replanted, and recent woodland
Authors: Swallow Kelly A. , Wood Matt J. , Goodenough Anne E.
Published: May 2020

Questions

The floristic distinctiveness of ancient woodland relative to recent woodland is commonly measured by Ancient Woodland Indicator (AWI) species richness. However, focussing on a pre‐defined subset of species means that wider community‐level differences may be overlooked. Can ancient semi‐natural, ancient replanted, and recent woodland herb layer communities be distinguished by alpha, beta, and gamma diversity? How are any differences partitioned across AWI and non‐AWI species communities?

Location

Cotswolds, southwest UK.

Methods

To quantify AWI and non‐AWI responses to stand history in ancient semi‐natural, ancient replanted, and recent woodland, we conducted floristic surveys of 45 sites. Using a modelling approach, we tested the relative and additive contribution of alpha‐scale AWI and non‐AWI species richness to woodland distinctiveness. Ordination was applied to analyse beta species composition distinctiveness, and multilevel pattern analysis was used to examine which species were significant contributors to gamma‐scale richness differences.

Results

AWI species richness models significantly distinguished ancient semi‐natural woodland from both ancient replanted and recent woodland at the alpha scale. For the classification of ancient semi‐natural woodland and recent woodland, the hierarchical inclusion of non‐AWI alpha richness resulted in a superior and more significant model. AWI gamma richness was numerically similar for all three woodland categories, whereas non‐AWI was more varied. AWI and non‐AWI species composition showed significant beta diversity differences among all woodland types, with six species being significant drivers of differences.

Conclusions

Our results have revealed previously undetected complexity in the contributions of AWI and non‐AWI species to floristic distinctiveness of ancient woodland. In addition to traditional AWI species, the non‐AWI assemblage also exhibited a sensitivity to habitat continuity that: (a) adds weight to the argument that ancient woodland is floristically distinct from recent woodland; and (b) provides a useful measure of success for ancient replanted woodland restoration.
Subfossil oribatid mite communities indicate Holocene permafrost dynamics in Canadian mires
Authors: Markkula Inkeri , Kuhry Peter
Published: May 2020

Permafrost thaw in peatlands is one of the most widespread and worrying consequences of climate warming in the sub‐Arctic area. To predict future climate feedbacks, it is important to study the history of permafrost aggradation and thaw. Plant macrofossil analysis with radiocarbon dating has been widely used in detecting past permafrost dynamics in peatlands, however, due to a lack of permafrost‐specific plant indicator species, determining the exact timing of permafrost aggradation remains a challenge. In this study, we investigated if oribatid mites can be used to determine Holocene permafrost aggradation and degradation in Canadian mires. Based on analyses of subfossil oribatid mite assemblages of Holocene peat profiles from two mires in the Hudson Bay Lowlands area, our results suggest that two species, Carabodes labyrinthicus and Neoribates aurantiacus, are useful bioindicators, which can be used in palaeoecological studies determining permafrost histories. Moreover, our results show that subfossil oribatid mite remains can reveal periods of permafrost, which cannot be determined with certainty based on plant macrofossils alone.
FAM111B enhances proliferation of KRAS‐driven lung adenocarcinoma by degrading p16
Authors: Kawasaki Keisuke , Nojima Satoshi , Hijiki Sachiko , Tahara Shinichiro , Ohshima Kenji , Matsui Takahiro , Hori Yumiko , Kurashige Masako , Umeda Daisuke , Kiyokawa Hiroki , Kido Kansuke , Okuzaki Daisuke , Morii Eiichi
Published: May 2020

Lung cancer is a common type of cancer that represents a health problem worldwide; lung adenocarcinoma (LUAD) is a major subtype of lung cancer. Although several treatments for LUAD have been developed, the mortality rate remains high because of uncontrollable progression. Further biological and clinicopathological studies are therefore needed. Here, we investigated the role of family with sequence similarity 111 member B (FAM111B), which is highly expressed in papillary‐predominant LUAD; however, its role in cancer is unclear. An immunohistochemical analysis confirmed that papillary‐predominant adenocarcinomas exhibited higher expression of FAM111B, compared with lepidic‐predominant adenocarcinomas. Additionally, FAM111B expression was significantly correlated with clinical progression. In vitro functional analyses using FAM111B‐knockout cells demonstrated that FAM111B plays an important role in proliferation and cell cycle progression of KRAS‐driven LUAD under serum‐starvation conditions. Furthermore, FAM111B regulated cyclin D1‐CDK4‐dependent cell cycle progression by degradation of p16. In summary, we revealed the clinical importance of FAM111B in human tumor tissues, as well as its function as a degradative enzyme. Therefore, FAM111B has potential as a clinicopathological prognostic marker for LUAD.
KinomeRun: An interactive utility for kinome target screening and interaction fingerprint analysis towards holistic visualization on kinome tree
Authors: Ansar Samdani , Vetrivel Umashankar
Published: May 2020

Kinases are key targets for many of the pathological conditions. Inverse screening of ligands serves as an essential mode to identify potential kinase targets in modern drug discovery research. Hence, we intend to develop KinomeRun, a robust pipeline for inverse screening and kinome tree visualization through the seamless integration of kinome structures, docking and kinome–drug interaction fingerprint analysis. In this pipeline, the hurdle of residue numbering in kinome is also resolved by creating a common index file with the conserved kinase pocket residues for comparative interaction analysis. KinomeRun can be used to screen the ligands of interest docked against multiple kinase structures in parallel around the kinase binding site and also to filter out the targets with unique interaction patterns. This automation is essential for prioritization of kinase targets that show specificity for a given drug and will also serve as a crucial tool kit for holistic approaches in kinase drug discovery. KinomeRun is developed using python and bash programming language and is distributed freely under the GNU GPL licence‐3.0 and can be downloaded at https://github.com/inpacdb/KinomeRun. The tutorial videos for installation, target screening and customized filtration are available at https://www.youtube.com/playlist?list=PLuIaEFtMVgQ7v__WigQH9ilGVxrfI1LKs and also be downloaded for offline viewing from the github link.
Targeting the interleukin‐7 receptor alpha by an anti‐CD127 monoclonal antibody improves allergic airway inflammation in mice
Authors: Mai Hoa Le , Nguyen Thi Van Ha , Bouchaud Grégory , Henrio Kelly , Cheminant Marie‐Aude , Magnan Antoine , Brouard Sophie
Published: May 2020

Background

Interleukin‐7 (IL‐7) is the most important cytokine for T‐cell homeostasis. IL‐7 signals through the IL‐7 receptor (IL‐7R) which is composed of an alpha chain (IL‐7Rα), also called CD127 and a common gamma chain. T lymphocytes, especially T helper type 2, play a crucial role in the pathobiology of allergic asthma.

Objective

To study the effects of an anti‐CD127 monoclonal antibody (mAb) in a murine model of allergic airway inflammation induced by house dust mite (HDM).

Methods

Allergic airway inflammation was induced in mice using a protocol comprising 4 weekly percutaneous sensitizations followed by 2 weekly intranasal challenges with total HDM extracts and treated by intraperitoneal injections of an anti‐CD127 mAb. Because CD127 is shared by both IL‐7R and the receptor for thymic stromal lymphopoietin (TSLP), a group of mice was also treated with an anti‐IL‐7 mAb to block only the IL‐7 signalling pathway.

Results

Anti‐CD127 mAb‐treated mice showed significantly lower airway resistance in response to methacholine and improvement in lung histology compared with isotype mAb‐treated animals. Anti‐CD127 mAb treatment significantly decreased the mRNA expression of Th2 cytokines (IL‐4, IL‐5, and IL‐13) and chemokines (CCL5/RANTES) in lung tissue, decreased the secretion of Th2 cytokines (IL‐4, IL‐5, and IL‐13) and chemokines (CXCL1 and CCL11/eotaxin) in bronchoalveolar lavage fluid (BALF), decreased serum HDM‐specific IgE, and reduced the number of total leucocytes and leucocyte subpopulations such as eosinophils, macrophages, lymphocytes, T lymphocytes, and ILC2 in BALF and lung tissue. Mice treated with anti‐IL‐7 mAb also showed less allergic airway inflammation as evidenced by significantly lower airway resistance and fewer leucocytes in BALF and lung tissue compared to mice treated with the corresponding isotype control mAb.

Conclusion and Clinical Relevance

Targeting the IL‐7Rα by an anti‐CD127 mAb improves allergic airway inflammation in mice and presents as a potential therapeutic approach for allergic asthma.
Persistent viral shedding of SARS‐CoV‐2 in faeces – a rapid review
Authors: Gupta S. , Parker J. , Smits S. , Underwood J. , Dolwani S.
Published: May 2020

Aim

In addition to respiratory symptoms, COVID‐19 can present with gastrointestinal complaints suggesting possible faeco‐oral transmission. The primary aim of this review was to establish the incidence and timing of positive faecal samples for SARS‐CoV‐2 in patients with COVID‐19.

Methods

A systematic literature review identified studies describing COVID‐19 patients tested for faecal virus. Search terms for MEDLINE included ‘clinical’, ‘faeces’, ‘gastrointestinal secretions’, ‘stool’, ‘COVID‐19’, ‘SARS‐CoV‐2’ and ‘2019‐nCoV’. Additional searches were done in the American Journal of Gastroenterology, Gastroenterology, Gut, Lancet Gastroenterology and Hepatology, the World Health Organization Database, the Centre for Evidence‐Based Medicine, New England Journal of Medicine, social media and the National Institute for Health and Care Excellence, bioRxiv and medRxiv preprints. Data were extracted concerning the type of test, number and timing of positive samples, incidence of positive faecal tests after negative nasopharyngeal swabs and evidence of viable faecal virus or faeco‐oral transmission of the virus.

Results

Twenty‐six relevant articles were identified. Combining study results demonstrated that 53.9% of those tested for faecal RNA were positive. The duration of faecal viral shedding ranged from 1 to 33 days after a negative nasopharyngeal swab with one result remaining positive 47 days after onset of symptoms. There is insufficient evidence to suggest that COVID‐19 is transmitted via faecally shed virus.

Conclusion

There is a high rate of positive polymerase chain reaction tests with persistence of SARS‐CoV‐2 in faecal samples of patients with COVID‐19. Further research is needed to confirm if this virus is viable and the degree of transmission through the faeco‐oral route. This may have important implications on isolation, recommended precautions and protective equipment for interventional procedures involving the gastrointestinal tract.