bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid Fluorogenic Enumeration of Escherichia coli in Selected, Naturally Contaminated High Moisture Foods
Authors: Poelma Paul L , Wilson Clyde R , Andrews Wallace H
Published: February 2020

An assay for the enzyme glucuronidase was used to determine the presence of Escherichia coli in selected, naturally contaminated high moisture foods. Raw pork sausage, ground turkey, and ground beef were inoculated into tubes containing the substrate 4-methylumbelliferyl beta-D-glucuronide (MUG) in lauryl tryptose (LT) medium. After incubation at 35°C for 24 h, the inoculated LT-MUG tubes were examined under longwave ultraviolet light for the presence of a fluorogenic glucuronidase end product. A fluorescing tube indicated the presumptive presence of E. coli. The 10 day most probable number method of the AOAC and the LT-MUG procedure gave comparable recoveries of E. coli.
Brucella Endocarditis in Persons Who Inject Drugs
Authors: Cafardi John M , Haas Douglas , Lamarre Thomas , Feinberg Judith
Published: February 2020

We report 2 cases of infective endocarditis in injection drug users due to Brucella infection. Although cardiac involvement is a frequent sequela of brucellosis and endocarditis is often seen with injection drug use, Brucella endocarditis in persons who inject drugs without zoonotic exposure has not been reported to date.
Apatinib treatment for unresectable gastrointestinal stromal tumor with synchronous gastric cancer
Authors: Xu Huanji , Zhou Sheng , Hu Qiancheng , Cao Dan
Published: February 2020

Nearly one-fifth of patients diagnosed with gastrointestinal stromal tumors (GISTs) simultaneously experience a second primary tumor. In particular, coexistence of gastric GISTs and gastric cancer is relatively more common. However, the optimal treatment for advanced GIST with gastric cancer is largely unknown. We report a case of simultaneous occurrence of gastric GIST and gastric cancer that benefited from apatinib. After first-line imatinib and S-1 treatment for 6 months, the GIST and the gastric cancer both progressed. The patient was then treated with apatinib, exhibiting a partial response (PR) both in the GIST and the gastric cancer at 7 months, and continuous PR so far with well-controlled toxic effects of hypertension. Progression-free survival reached 10 months. In view of the relatively high incidence of advanced GIST with synchronous gastric cancer, therapy to simultaneously treat the two kinds of tumors is urgently needed. Apatinib provides promising and well-tolerated therapy for GISTs with synchronous gastric cancer refractory to chemotherapy combined with imatinib.
ASSESSMENT OF AMBIENT NEUTRON DOSE EQUIVALENT IN SPATIALLY FRACTIONATED RADIOTHERAPY WITH PROTONS USING PHYSICAL COLLIMATORS
Authors: Charyyev Serdar , Wang C-K Chris
Published: February 2020

New technique is trending in spatially fractionated radiotherapy with protons to utilize the spot scanning together with a physical collimator to obtain minibeams. The primary goal of this study is to quantify ambient neutron dose equivalent (${H}^{\ast }(10)$) due to the secondary neutrons when physical collimator is used to achieve desired minibeams. The ${H}^{\ast }(10)$ per treatment proton dose (D) was assessed using Monte Carlo code TOPAS and measured using WENDI-II detector at different angles (135, 180, 225 and 270 degrees) and distances (11 cm, 58 and 105 cm) from the phantom for two cases: with and without physical collimation. Without collimation $\frac{H^{\ast }(10)}{D}$ varied from 0.0013 to 0.242 mSv/Gy. With collimation $\frac{H^{\ast }(10)}{D}$ varied from 0.017 to 3.23 mSv/Gy. Results show that the secondary neutron dose will increase tenfold when the physical collimator is used. Regardless, it will be low and comparable to the neutron dose produced by conventional passive-scattered proton beams.
Trade-offs between host tolerances to different pathogens in plant–virus interactions
Authors: Montes Nuria , Vijayan Viji , Pagán Israel
Published: February 2020

Although accumulating evidence indicates that tolerance is a plant defence strategy against pathogens as widespread as resistance, how plants evolve tolerance is poorly understood. Theory predicts that hosts will evolve to maximize tolerance or resistance, but not both. Remarkably, most experimental works failed in finding this trade-off. We tested the hypothesis that the evolution of tolerance to one virus is traded-off against tolerance to others, rather than against resistance and identified the associated mechanisms. To do so, we challenged eighteen Arabidopsis thaliana genotypes with Turnip mosaic virus (TuMV) and Cucumber mosaic virus (CMV). We characterized plant life-history trait modifications associated with reduced effects of TuMV and CMV on plant seed production (fecundity tolerance) and life period (mortality tolerance), both measured as a norm of reaction across viral loads (range tolerance). Also, we analysed resistance-tolerance and tolerance-tolerance trade-offs. Results indicate that tolerance to TuMV is associated with changes in the length of the pre-reproductive and reproductive periods, and tolerance to CMV with resource reallocation from growth to reproduction; and that tolerance to TuMV is traded-off against tolerance to CMV in a virulence-dependent manner. Thus, this work provides novel insights on the mechanisms of plant tolerance and highlights the importance of considering the combined effect of different pathogens to understand how plant defences evolve.
12Psychoanalysis
Authors: Arnold Lucy
Published: February 2020

The intersection between psychoanalysis and politics, with their shared investment in the dynamics of self–other relationships, emerged as a key concern in psychoanalytic thinking in 2019. This year’s review examines five texts which explore this intersection through a diverse range of approaches and is divided into five sections: 1. Introduction; 2. Contemporary Subjects: Psychoanalysis in 2019, which examines Julia Kristeva’s, Passions of Our Time; 3. Mourning Subjects: Politics and Psychoanalysis, which reviews Stephen Frosh, Those Who Come After: Postmemory, Acknowledgement and Forgiveness and Noëlle McAfee, Fear of Breakdown: Politics and Psychoanalysis alongside Conrad Chrzanowski’s article, ‘The Group’s Vulnerability to Disaster: Basic Assumptions and Work Group Mentalities Underlying Trump’s 2016 Election’; 4. Creative Subjects: Psychoanalysis and Visual Art, where I consider Patricia Townsend, Creative States of Mind: Psychoanalysis and the Artist’s Process, with Alberto Stefana’s article, ‘Revisiting Marion Milner’s Work on Creativity and Art’; and 5. Dis-membered Subjects: Psychoanalysis at the Margins, which explores Gabrielle Brown (ed.), Psychoanalytic Thinking on the Unhoused Mind.
Intermittent gross hematuria after lithotripsy: ureteral stent or residual stone?
Authors: Peng Linjie , Wen Junjun , Zhong Wen
Published: February 2020

Purpose

To explore the role of stone fragment and ureteric stent in process of intermittent gross hematuria (IGH), discuss the definition of ureteral stent related symptoms (USS) in a setting of lithotripsy and clinical outcomes of IGH.

Methods

Between January 2018 and July 2019, patients with completed one month follow up after lithotripsy were collected. Based on whether occurrence of IGH, demographics, stent information and clinical outcomes were mainly analyzed.

Results

A total of 258 consecutive patients were eventually analyzed, among which 97 patients (37.6%) suffered from IGH. Compared to patients without symptom of IGH, preoperative potassium level (3.89±0.43mmol/L vs. 4.02±0.42mmol/L, p=0.01), initial stone free rate (SFR, 50.52% vs. 68.32%, p=0.007) and potassium citrate application (11.34% vs. 4.55%, p=0.04) were found statistically different in univariate analysis. In multivariate logistic analysis, preoperative potassium level (OR: 0.39, CI: 0.19-0.76, p=0.007), potassium citrate (OR: 2.96, CI: 1.07-8.73, p=0.04), initial SFR (OR: 0.42, CI: 0.24-0.74, p<0.001), and hospital stay (OR: 0.94, CI: 0.89-0.99, p=0.045) were independent risk factors, rather than stent size and stent position. Hemoglobin change, stone area reduction and SFR in one-month follow-up were similar between groups, but more outpatient consultations were found in hematuria group (20 vs. 3, p<0.001), among which 2 patients were readmitted for severe ongoing hematuria.

Conclusions

Stone fragment, rather the size or length of ureteral stent, is the independent risk factors of IGH. Definition of USS is not suitable for IGH after lithotripsy, and a comprehensive inform and enough rest would reduce the unnecessary medical consultations.
Analysis of meteorological conditions and prediction of epidemic trend of 2019-nCoV infection in 2020
Authors: Bu Jin , Peng Dong-Dong , Xiao Hui , Yue Qian , Han Yan , Lin Yu , Hu Gang , Chen Jing
Published: February 2020

Objective

To investigate the meteorological condition for incidence and spread of 2019-nCoV infection, to predict the epidemiology of the infectious disease, and to provide a scientific basis for prevention and control measures against the new disease.

Methods

The meteorological factors during the outbreak period of the novel coronavirus pneumonia in Wuhan in 2019 were collected and analyzed, and were confirmed with those of Severe Acute Respiratory Syndrome (SARS) in China in 2003. Data of patients infected with 2019-nCoV and SARS coronavirus were collected from WHO website and other public sources.

Results

This study found that the suitable temperature range for 2019-nCoV survival is (13-24 °C), among which 19°C lasting about 60 days is conducive to the spread between the vector and humans; the humidity range is 50%-80%, of which about 75% humidity is conducive to the survival of the coronavirus; the suitable precipitation range is below 30 mm/month. Cold air and continuous low temperature over one week are helpful for the elimination of the virus. The prediction results show that with the approach of spring, the temperature in north China gradually rises, and the coronavirus spreads to middle and high latitudes along the temperature line of 13-19 °C. The population of new coronavirus infections is concentrated in Beijing, Tianjin, Hebei, Jiangsu, Zhejiang, Shanghai and other urban agglomerations. Starting from May 2020, the Beijing-Tianjin-Hebei urban agglomeration, the Central China Zhengzhou-Wuhan urban agglomeration, the eastern Jiangsu-Zhejiang-Shanghai urban agglomeration, and the southern Pearl River Delta urban agglomeration are all under a high temperature above 24 °C, which is not conducive to the survival and reproduction of coronaviruses, so the epidemic is expected to end.

Conclusions

A wide range of continuous warm and dry weather is conducive to the survival of 2019-nCoV. The coming of spring, in addition to the original Wuhan-Zhengzhou urban agglomeration in central China, means that the prevention and control measures in big cities located in mid-latitude should be strengthened, especially the monitoring of transportation hubs. The Pearl River Delta urban agglomeration is a concentrated area of population in south China, with a faster temperature rise than those in mid-high latitudes, and thus the prevention in this area should be prioritized. From a global perspective, cities with a mean temperature below 24 °C are all high-risk cities for 2019-nCoV transmission before June.
Assessing the impact of reduced travel on exportation dynamics of novel coronavirus infection (COVID-19)
Authors: Anzai Asami , Kobayashi Tetsuro , Linton Natalie M , Kinoshita Ryo , Hayashi Katsuma , Suzuki Ayako , Yang Yichi , Jung Sung-mok , Miyama Takeshi , Akhmetzhanov Andrei R , Nishiura Hiroshi
Published: February 2020

The impact of the drastic reduction in travel volume within mainland China in January and February 2020 was quantified with respect to reports of novel coronavirus (COVID-19) infections outside China. Data on confirmed cases diagnosed outside China were analyzed using statistical models to estimate the impact of travel reduction on three epidemiological outcome measures: (i) the number of exported cases, (ii) the probability of a major epidemic, and (iii) the time delay to a major epidemic. From 28 January to 7 February 2020, we estimated that 226 exported cases (95% confidence interval: 86, 449) were prevented, corresponding to a 70.4% reduction in incidence compared to the counterfactual scenario. The reduced probability of a major epidemic ranged from 7% to 20% in Japan, which resulted in a median time delay to a major epidemic of two days. Depending on the scenario, the estimated delay may be less than one day. As the delay is small, the decision to control travel volume through restrictions on freedom of movement should be balanced between the resulting estimated epidemiological impact and predicted economic fallout.
Estimating the Efficacy of Quarantine and Traffic Blockage for the Epidemic Caused by 2019-nCoV (COVID-19):A Simulation Analysis
Authors: Li Deqiang , Liu Zhicheng , Liu Qinghe , Gao Zefei , Zhu Junkai , Yang Junyan , Wang Qiao
Published: February 2020

Background

Since the 2019-nCoV (COVID-19) outbreaks in Wuhan, China, the cumulative number of confirmed cases is increasing every day, and a large number of populations all over the world are at risk. The quarantine and traffic blockage can alleviate the risk of the epidemic and the infections, henceforth evaluating the efficacy of such actions is essential to inform policy makers and raise the public awareness of the importance of self-isolation and quarantine.

Method

We collected confirmed case data and the migration data, and introduced the quarantine factor and traffic blockage factor to the Flow-SEIR model. By varying the quarantine factor and traffic blockage factor, we simulated the change of the peak number and arrival time of infections, then the efficacy of these two intervation measures can be analyzed in our simulation. In our study, the self-protection at home is also included in quarantine.

Results

In the simulated results, the quarantine and traffic blockage are effective for epidemic control. For Hubei province, the current quarantine factor is estimaed to be 0.405, which means around 40.5% of suceptibles who are close contacting with are in quarantine, and the current traffic blockage factor is estimaed to be 0.66, which indicates around 34% of suceptibles who had flowed out from Hubei. For the other provinces outside Hubei, the current quarantine factor is estimated to be 0.285, and the current traffic blockage factor is estimated to be 0.26. With the quarantine and traffic blockage factor increasing, the number of infections decrease dramatically. We also simulated the start dates of quarantine and traffic blockage at four time points, the simulated results show that the early of warning is also effective for epidemic containing. However, provincial level traffic blockage can only alleviate 21.06% - 22.38% of the peak number of infections. In general, the quarantine is much more effective than the traffic blockage control.

Conclusion

Both of quarantine and traffic blockage are effective ways to control the spread of COVID-19. However, the eff icacy of quarantine is found to be much stronger than that of traffic blockage. Considering traffic blockage may also cause huge losses of economy, we propose to gradually deregulate the traffic blockage, and improve quarantine instead. Also, there might be a large number of asymptomatic carriers of COVID-19, the quarantine should be continued for a long time until the epidemic is totally under control.
SMPD1 variants do not have a major role in REM sleep behavior disorder
Authors: Rudakou Uladzislau , Futhey Naomi C. , Krohn Lynne , Ruskey Jennifer A. , Heilbron Karl , Cannon Paul ,   The 23andMe Research Team, Alam Armaghan , Arnulf Isabelle , Hu Michele T.M. , Montplaisir Jacques Y. , Gagnon Jean-François , Desautels Alex , Dauvilliers Yves , Toffoli Marco , Gigli Gian Luigi , Valente Mariarosaria , Högl Birgit , Stefani Ambra , Holzknecht Evi , Sonka Karel , Kemlink David , Oertel Wolfang , Janzen Annette , Plazzi Giuseppe , Antelmi Elena , Figorilli Michela , Puligheddu Monica , Mollenhauer Brit , Trenkwalder Claudia , Sixel-Döring Friederike , De Cock Valérie Cochen , Monaca Christelle Charley , Heidbreder Anna , Ferini-Strambi Luigi , Dijkstra Femke , Viaene Mineke , Beatriz Abril , Boeve Bradley F. , Postuma Ronald B. , Rouleau Guy A. , Gan-Or Ziv
Published: February 2020

Mutations in the sphingomyelin phosphodiesterase 1 (SMPD1) gene were reported to be associated with Parkinson disease (PD) and dementia with Lewy bodies (DLB). The majority of patients with isolated rapid eye movement sleep behavior disorder (iRBD) develop PD or DLB later in life, suggesting that iRBD is a prodromal phase of these two conditions. In the current study we aimed to evaluate the role of SMPD1 variants in iRBD. SMPD1 and its untranslated regions were sequenced using targeted next-generation sequencing in 959 iRBD patients and 1,287 controls from European descent. Logistic regression adjusted for sex and age showed no significant associations with two common variants and iRBD (rs1050239 and rs8164). The frequency of all rare nonsynonymous SMPD1 variants (minor allele frequency <1%) was found to be twice as high in cases than in controls (1.46% vs. 0.70%, Fisher’s exact test p=0.09) but there was no statistically significant burden (p=0.64). Our study reports no statistically significant association of SMPD1 variants and iRBD. It is hence unlikely that SMPD1 plays a major role in iRBD.
Organoid Polymer Functionality and Mode ofKlebsiella PneumoniaeMembrane Antigen Presentation Regulates Ex Vivo Germinal Center Epigenetics in Young and Aged B Cells
Authors: Graney Pamela L. , Lai Kristine , Post Sarah , Brito Ilana , Cyster Jason , Singh Ankur
Published: February 2020

Antibiotic-resistant bacteria are a major global health threat that continues to rise due to a lack of effective vaccines. Of concern areKlebsiella pneumoniaethat fail to inducein vivogerminal center B cell responses, which facilitate antibody production to fight infection. Immunotherapies using antibodies targeting antibiotic-resistant bacteria are emerging as promising alternatives, however, cannot be efficiently derived ex vivo, necessitating the need for immune technologies to develop therapeutics. Here, four-arm PEG-organoids were developed to elucidate the effects of polymer end-point chemistry, integrin ligands, and mode ofK. pneumoniaeantigen presentation on germinal center-like B cell epigenetics, to better define the cell-microenvironment factors regulatingex vivogerminal center dynamics. Notably, PEG vinyl sulfone or acrylate failed to sustain primary immune cells, but functionalization with maleimide (PEG-4MAL) led to B cell expansion and germinal center-like induction. RNA sequencing analysis of lymph node stromal and germinal center B cells showed niche associated heterogeneity of integrin-related genes. Incorporation of niche-mimicking bioadhesive peptides revealed that collagen 1 mimicking peptides promoted germinal center-like dynamics and epigenetics. PEG-4MAL organoids elucidated the impact ofK. pneumoniaemembrane embedded protein antigen versus soluble antigen presentation on germinal center-like activation and preserved the response across young and aged mice.
Granulocyte-Colony Stimulating Factor reduces cocaine-seeking and downregulates glutamatergic synaptic proteins in medial prefrontal cortex
Authors: Hofford Rebecca S. , Euston Tanner J. , Wilson Rashaun S. , Meckel Katherine R. , Peck Emily G. , Godino Arthur , Landry Joseph A. , Calipari Erin S. , Lam TuKiet T. , Kiraly Drew D.
Published: February 2020

Background

Psychostimulant use disorder is a major public health issue, and despite the scope of the problem there are currently no FDA approved treatments. There would be tremendous utility in development of a treatment that could help patients both achieve and maintain abstinence. Previous work from our group has identified granulocyte-colony stimulating factor (G-CSF) as a neuroactive cytokine that alters behavioral response to cocaine, increases synaptic dopamine release, and enhances cognitive flexibility. Here, we investigate the role of G-CSF in affecting extinction and reinstatement of cocaine-seeking and perform detailed characterization of its proteomic effects in multiple limbic substructures.

Methods

Sprague-Dawley rats were injected with PBS or G-CSF during (1) extinction or (2) abstinence from cocaine self-administration, and drug seeking behavior was measured. Quantitative assessment of changes in the proteomic landscape in the nucleus accumbens (NAc) and medial prefrontal cortex (mPFC) were performed via data-independent acquisition (DIA) mass spectrometry analysis.

Results

Administration of G-CSF during extinction accelerated the rate of extinction, and administration during abstinence attenuated cue-induced cocaine-seeking. Analysis of global protein expression demonstrated that G-CSF regulated proteins primarily in mPFC that are critical to glutamate signaling and synapse maintenance.

Conclusion

Taken together, these findings support G-CSF as a viable translational research target with the potential to reduce drug craving or seeking behaviors. Importantly, recombinant G-CSF exists as an FDA-approved medication which may facilitate rapid clinical translation. Additionally, using cutting-edge multi-region discovery proteomics analyses, these studies identify a novel mechanism underlying G-CSF effects on behavioral plasticity.
Identification of multiple noise sources improves estimation of neural responses across stimulus conditions
Authors: Weber Alison I. , Shea-Brown Eric , Rieke Fred
Published: February 2020

Most models of neural responses are constructed to capture the average response to inputs but poorly reproduce the observed response variability. The origins and structure of this variability have significant implications for how information is encoded and processed in the nervous system. Here, we present a new modeling framework that better captures observed features of neural response variability across stimulus conditions by incorporating multiple sources of noise. We use this model to fit responses of retinal ganglion cells at two different ambient light levels and demonstrate that it captures the full distribution of responses. The model reveals light level-dependent changes that could not be seen with previous models. It shows both large changes in rectification of nonlinear circuit elements and systematic differences in the contributions of different noise sources under different conditions. This modeling framework is general and can be applied to a variety of systems outside the retina.
Extraction of Protein Dynamics Information Hidden in Cryogenic Electron Microscopy Maps Using Deep Learning
Authors: Matsumoto Shigeyuki , Ishida Shoichi , Araki Mitsugu , Kato Takayuki , Terayama Kei , Okuno Yasushi
Published: February 2020

Technical breakthroughs in cryogenic electron microscopy (cryo-EM)-based single-particle analysis have enabled the structures of numerous proteins to be solved at atomic or near-atomic resolutions, including extremely large macromolecules whose structures could not be solved by conventional techniques. Determining the dynamics properties of these macromolecules, based on their solved structures, can further improve our understanding of their functional mechanisms. However, such analysis is often hampered by the large molecular size and complex structural assembly, making both experimental and computational approaches to determine dynamics properties challenging. Here, we report a deep learning-based approach, DEFMap, to extract the dynamics information “hidden” in cryo-EM density maps. By relying only on cryo-EM maps, DEFMap successfully provided dynamics information equivalent to that determined from molecular dynamics (MD) simulations and experimental approaches at the atomic and residue levels. Additionally, DEFMap could detect dynamics changes associated with molecular recognition and the accompanying allosteric conformational stabilizations, which trigger various biological events such as signal transduction and enzyme catalysis. This approach will provide new insights into the functional mechanisms of biological molecules, accelerating modern molecular biology researches. Furthermore, this advanced strategy combining experimental data, deep learning approaches, and MD simulations would open a new multidisciplinary science area
Experimentally determined long intrinsically disordered protein regions are now abundant in the Protein Data Bank
Authors: Monzon Alexander Miguel , Necci Marco , Quaglia Federica , Walsh Ian , Piovesan Damiano , Zanotti Giuseppe , Tosatto Silvio C. E.
Published: February 2020

Intrinsically disordered protein regions are commonly defined from missing electron density in X-ray structures. Experimental evidence for long disorder regions (LDRs) of at least 30 residues was so far limited to a less than a thousand manually curated proteins. Here, we describe a comprehensive and large-scale analysis of experimental LDRs for 3,133 unique proteins, demonstrating an increasing coverage of intrinsic disorder in the Protein Data Bank (PDB) in the last decade. The results suggest that long missing residue regions are a good quality source to annotate intrinsically disordered regions and perform functional analysis in large data sets. The consensus approach used to define LDRs allows to evaluate context dependent disorder and provide a common definition at the protein level.
Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway
Authors: Gillies Taryn E. , Pargett Michael , Silva Jillian M. , Teragawa Carolyn , McCormick Frank , Albeck John G.
Published: February 2020

Activating mutations in RAS are present in ∼30% of human tumors, and the resulting aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of these signaling changes is uncertain, with activating RAS mutants linked to both increased and decreased ERK activationin vivo. Rationally targeting the kinase activity of this pathway requires clarification of the quantitative effects of RAS mutations. Here, we use live-cell imaging in cell lines expressing only one RAS isoform to quantify ERK activity with a new level of accuracy. We find that despite large differences in their biochemical activity, mutant KRAS isoforms within cells have similar ranges of ERK output. We identify roles for pathway-level effects, including variation in feedback strength and feedforward modulation of phosphatase activity, that act to rescale pathway sensitivity independent of expression level, ultimately resisting changes in the dynamic range of ERK activity while preserving responsiveness to growth factor stimuli. Our results reconcile seemingly inconsistent reports within the literature and imply that the initial signaling changes induced by RAS mutations in oncogenesis are subtle.
Systematic quantification of synapses in primary neuronal culture
Authors: Verstraelen Peter , Garcia Gerardo , Verschuuren Marlies , Asselbergh Bob , Nuydens Rony , Larsen Peter , Timmermans Jean-Pierre , De Vos Winnok H.
Published: February 2020

A vast set of neurological disorders is associated with impaired synaptic connectivity. Therefore, modulation of synapse formation could have therapeutic relevance. However, the high density and small size of synapses make their quantification a challenging task. To improve the reliability of synapse-oriented drug screens, we evaluated a panel of synapse-targeting antibodies for their labeling specificity on hippocampal and cortical cell cultures using quantitative immunofluorescence microscopy. For those antibodies that passed multiparametric validation, we assessed pairwise colocalization, an often-used readout for established synapses. We found that even when two pan-synaptic markers were used, the overlap was incomplete, and the presence of spurious signals limited the dynamic range. To circumvent this problem, we implemented a proximity ligation-based approach, that only leads to a signal when two pre- and postsynaptic markers are sufficiently close. We demonstrate that this approach can be applied to different synaptic marker combinations and can be successfully used for quantification of synapse density in cultures of different maturity stage in healthy or pathological conditions. Thus, the unbiased analysis of synapse labeling and exploitation of resident protein proximity, allows increasing the sensitivity of synapse quantifications in neuronal culture and therefore represents a valuable extension of the analytical toolset forin vitrosynapse screens.
Stony coral populations are more sensitive to changes in vital rates in disturbed environments
Authors: Hall Tessa E. , Freedman Andrew S. , de Roos André M. , Edmunds Peter J. , Carpenter Robert C. , Gross Kevin
Published: February 2020

Reef-building corals, like many long-lived organisms, experience environmental change as a combination of separate but concurrent processes, some of which are gradual yet long-lasting, while others are more acute but short-lived. For corals, some chronic environmental stressors, such as rising temperature and ocean acidification, are thought to induce gradual changes in colonies’ vital rates. Meanwhile, other environmental changes, such as the intensification of tropical cyclones, change the disturbance regime that corals experience. Here, we use a physiologically structured population model to explore how chronic environmental stressors that impact the vital rates of individual coral colonies interact with the intensity and magnitude of disturbance to affect coral population dynamics and cover. We find that when disturbances are relatively benign, intraspecific density dependence driven by space competition partially buffers coral populations against gradual changes in vital rates. However, the impact of chronic stressors is amplified in more highly disturbed environments, because disturbance weakens the buffering effect of space competition. We also show that coral cover is more sensitive to changes in colony growth and mortality than to external recruitment, at least in non-self-seeding populations, and that space competition and size structure mediate the extent and pace of coral-population recovery following a large-scale mortality event. Understanding the complex interplay among chronic environmental stressors, mass-mortality events, and population size structure sharpens our ability to project coral dynamics in an increasingly disturbed future.
KD-64 – a new selective A2Aadenosine receptor antagonist has anti-inflammatory activity but contrary to the non-selective antagonist – caffeine does not reduce diet-induced obesity in mice
Authors: Kotańska Magdalena , Dziubina Anna , Szafarz Małgorzata , Mika Kamil , Reguła Karolina , Bednarski Marek , Zygmunt Małgorzata , Drabczyńska Anna , Sapa Jacek , Kieć-Kononowicz Katarzyna
Published: February 2020

The A2adenosine receptors play an important role, among others, in the regulation of inflammatory process and glucose homeostasis in diabetes and obesity. Thus, the presented project evaluated of influence of the selective antagonist of A2Aadenosine receptor – KD-64 as compared to the known non-selective antagonist – caffeine on these two particular processes. Two different inflammation models were induced namely local and systemic inflammation. Obesity was induced in mice by high-fat diet and the tested compounds (KD-64 and caffeine) were administrated for 21 days. KD-64 showed anti-inflammatory effect in both tested inflammation models and administered at the same dose as ketoprofen exerted stronger effect than this reference compound. Elevated levels of IL-6 and TNF-α observed in obese control mice were significantly lowered by the administration of KD-64 and were similar to the values observed in control non-obese mice. Interestingly, caffeine increased the levels of these parameters. In contrast to caffeine which had no influence on AlaT activity, KD-64 administration significantly lowered AlaT activity in the obese mice. Although, contrary to caffeine, KD-64 did not reduce diet-induced obesity in mice, it improved glucose tolerance. Thus, the activity of the selective adenosine A2Areceptor antagonist was quite different from that of the non-selective.
Mechanism of upstream promoter element stimulation of transcription at a ribosomal RNA promoter determined by single-molecule imaging
Authors: Mumm Jeffrey P. , Friedman Larry J. , Gelles Jeff
Published: February 2020

DNA elements upstream of transcription promoters play a role in regulating transcription initiation in all organisms. In bacteria, upstream A-T rich sequences called UP elements can stimulate transcription through contact with the α subunit C-terminal domain (αCTD) of core RNA polymerase (RNAP), but the kinetic mechanisms by which they do so remain unclear. We investigated the role of the UP element in stimulating initiation from the strong E. coli 16s rRNA promoter using single-molecule fluorescence microscopy to visualize σ70RNAP holoenzyme binding and the formation nascent RNA by oligonucleotide probe hybridization on individual DNA molecules containing therrnBP1 promoter. By directly detecting initial binding of σ70RNAP to promoter and monitoring the lifetimes of promoter-polymerase complexes, the experiments reveal the kinetic mechanism of polymerase recruitment to the promoter and the subsequent conformational change that stabilizes binding. The presence of UP stimulated the rate of initial binding of polymerase to promoter by at least six-fold, and this stimulation was fully sufficient to account for the increase in initiation rate by UP. Thus, UP likely functions at this strong promoter simply by acting as a binding target for the rapidly reorienting αCTD domain tethered to the core polymerase. In contrast, there were only minor effects of UP on the measured rates of the conformational change or the dissociation rates of the initial σ70RNAP promoter complexes. These studies define a paradigmatic kinetic mechanism for stimulation of transcription initiation by direct αCTD-DNA interactions. This mechanism can serve as a building block of more complex regulatory architectures in which αCTD promotes transcription through interactions with both DNA and protein activators.
AtCIPK16 Mediates Salt Stress Through Phytohormones and Transcription Factors
Authors: Amarasinghe Shanika L. , Huang Wenmian , Watson-Haigh Nathan S. , Gilliham Matthew , Roy Stuart J. , Baumann Ute
Published: February 2020

Soil salinity causes large productivity losses for agriculture worldwide. “Next-generation crops” that can tolerate salt stress are required for the sustainability of global food production. Previous research inArabidopsis thalianaaimed at uncovering novel factors underpinning improved plant salinity tolerance identified the protein kinase AtCIPK16. Overexpression ofAtCIPK16enhanced shoot Na+exclusion and increased biomass in both Arabidopsis and barley. Here, a comparative transcriptomic study on Arabidopsis lines expressingAtCIPK16was conducted in the presence and absence of salt stress, using an RNA-Seq approach, complemented by AtCIPK16 interaction and localisation studies. We are now able to provide evidence for AtCIPK16 activity in the nucleus. Moreover, the results manifest the involvement of a transcription factor, AtTZF1, phytohormones and the ability to quickly reach homeostasis as components important for improving salinity tolerance in transgenics overexpressingAtCIPK16. Furthermore, we suggest the possibility of both biotic and abiotic tolerance through AtCIPK16, and propose a model for the salt tolerance pathway elicited through AtCIPK16.
Renal tubule Cpt1a overexpression protects from kidney fibrosis by restoring mitochondrial homeostasis
Authors: Miguel Verónica , Tituaña Jessica , Herrero J.Ignacio , Herrero Laura , Serra Dolors , Cuevas Paula , Barbas Coral , Puyol Diego Rodríguez , Márquez-Expósito Laura , Ruiz-Ortega Marta , Castillo Carolina , Sheng Xin , Susztak Katalin , Ruiz-Canela Miguel , Salas-Salvadó Jordi , González Miguel A. Martínez , Ortega Sagrario , Ramos Ricardo , Lamas Santiago
Published: February 2020

Chronic kidney disease (CKD) remains a major epidemiological, clinical and biomedical challenge. During CKD, renal tubular epithelial cells (TECs) suffer a persistent inflammatory and profibrotic response. Fatty acid oxidation (FAO), the main source of energy for TECs, is reduced in kidney fibrosis and contributes to its pathogenesis. To determine if FAO gain-of-function (FAO-GOF) could protect from fibrosis, we generated a conditional transgenic mouse model with overexpression of the fatty acid shuttling enzyme carnitine palmitoyl-transferase 1 A (CPT1A) in TECs.Cpt1aknock-in (CPT1A KI) mice subjected to three different models of renal fibrosis (unilateral ureteral obstruction, folic acid nephropathy-FAN and adenine induced nephrotoxicity) exhibited decreased expression of fibrotic markers, a blunted pro-inflammatory response and reduced epithelial cell damage and macrophage influx. Protection from fibrosis was also observed when Cpt1a overexpression was induced after FAN. FAO-GOF restituted oxidative metabolism and mitochondrial number and enhanced bioenergetics increasing palmitate oxidation and ATP levels, changes also recapitulated in TECs exposed to profibrotic stimuli. Studies in patients evidenced decreased CPT1 levels and increased accumulation of short and middle chain acyl-carnitines, reflecting impaired FAO in human CKD. We propose that strategies based on FAO-GOF may constitute powerful alternatives to combat fibrosis inherent to CKD.

Graphical abstract

Overexpression of CPT1A impedes tubular epithelial renal cell dedifferentiation and a pro-fibrotic phenotype by restoring mitochondrial metabolic bioenergetics.
Twist-chair conformation of the tetraoxepane ring remains unchanged in tetraoxaspirododecane diamines
Authors: Khalilov Leonard M. , Mescheryakova Ekaterina S. , Bikmukhametov Kamil Sh. , Makhmudiyarova Natalia N. , Shangaraev Kamil R. , Tulyabaev Arthur R.
Published: February 2020

A detailed structural analysis has been performed forN,N′-bis(4-chlorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22Cl2N2O4, (I),N,N′-bis(2-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (II), andN,N′-bis(4-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (III). The seven-membered ring with two peroxide groups adopts a twist-chair conformation in all three compounds. The lengths of the C—N and O—O bonds are slightly shorter than the average statistical values found in the literature for azepanes and 1,2,4,5-tetraoxepanes. The geometry analysis of compounds (I)–(III), the topological analysis of the electron density at the (3, −1) bond critical points within Bader's quantum theory of `Atoms in molecules' (QTAIM) and NBO (natural bond orbital) analysis at the B3LYP/6-31G(d,2p) level of theory showed that there arenO→σ*(C—O),nN→σ*(C—O) andnO→σ*(C—N) stereoelectronic effects. The molecules of compounds (I) and (III) are packed in the crystals as zigzag chains due to strong N—H...O and C—H...O hydrogen-bond interactions, whereas the molecules of compound (II) form chains in the crystals bound by N—H...O, C—H...π and C—H...O contacts. All these data show that halogen atoms and their positions have a minimal effect on the geometric parameters, stereoelectronic effects and crystal packing of compounds (I)–(III), so that the twist-chair conformation of the tetraoxepane ring remains unchanged.
The crystal structures and Hirshfeld surface analyses of a cadmium(II) and a zinc(II) mononuclear complex of the new tetrakis-substituted pyrazine ligand N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)
Authors: Tesouro Vallina Ana , Stoeckli-Evans Helen
Published: February 2020

The whole molecule of the cadmium(II) complex, diiodido{N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3
N
2,N
1,N
6}cadmium(II), [CdI2(C36H40N6)], (I), of the ligand N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline) (L), is generated by a twofold rotation symmetry; the twofold axis bisects the cadmium atom and the nitrogen atoms of the pyrazine ring. The ligand coordinates in a mono-tridentate manner and the cadmium atom has a fivefold CdN3I2 coordination environment with a distorted shape. In the zinc(II) complex, dichlorido{N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3
N
2,N
1,N
6}zinc(II) dichloromethane 0.6-solvate, [ZnCl2(C36H40N6)]·0.6CH2Cl2, (II), ligand L also coordinates in a mono-tridentate manner and the zinc atom has a fivefold ZnN3Cl2 coordination environment with a distorted shape. It crystallized as a partial dichloromethane solvate. In the crystal of I, the complex molecules are linked by weak C—H...I contacts, forming ribbons propagating along [100]. In the crystal of II, the complex molecules are linked by a series of C—H...π interactions, forming layers lying parallel to the (1\overline{1}1) plane. In the crystals of both compounds there are metal–halide...π(pyrazine) contacts present. The Hirshfeld analyses confirm the importance of the C—H...halide contacts in the crystal packing of both compounds.
Monotonicity, linearity and symmetry in the price volatility–volume relationship
Authors: Fousekis Panos , Tzaferi Dimitra
Published: February 2020

Purpose

This paper aims to investigate the contemporaneous link between price volatility and trading volume in the futures markets of energy.

Design/methodology/approach

Non-parametric (local linear) regression models and formal statistical tests are used to assess monotonicity, linearity and symmetry. The data are daily price and volumes from five futures markets (West Texas Intermediate, Brent, gasoline, heating oil and natural gas) in the USA.

Findings

Trading volume and price volatility have, in all markets, a strong nonlinear relation to each other. There are violations of monotonicity locally but not globally. The qualitative nature of the price shocks may have implications for the trading activity locally.

Originality/value

To the authors’ best knowledge, this is the first manuscript that investigates simultaneously and formally all the three important issues (i.e. monotonicity, linearity and asymmetry) for the price volatility–volume relationship using a highly flexible nonparametric approach.
Demand for global health training and experiences among emergency medicine trainees in Australia and New Zealand
Authors: Mitchell Rob D , Mitchell Rebecca L , Phillips Georgina A , Jayaratnam Skandarupan , Jamieson Jennifer , O'Reilly Gerard M
Published: February 2020

Objective

Demand for global health (GH) training and experiences among emergency medicine trainees is unknown. The primary objective of the Trainee Interest in Global Health Training (TIGHT) study was to quantify the number of trainees interested in completing a rotation in a resource‐limited environment within a low‐ or middle‐income country during their specialty training.

Methods

A cross‐sectional study of trainees in seven specialty training programmes was conducted between August and October 2018. Data were collected using a voluntary, anonymous, self‐reporting, web‐based survey. This study describes the results of a planned sub‐group analysis of ACEM trainees.

Results

There were 203 respondents among 2525 ACEM trainees. Although only a small number (36/198, 18.2%) had undertaken a GH experience as a specialty trainee, 85.6% (167/195) were keen to do so. The vast majority of respondents (179/194, 87.1%) were interested or very interested in having their GH experience accredited for training, but 68.9% (133/193) reported that accessing a suitable placement was a barrier. More than 79% (147/186) expressed interest in undertaking an integrated GH training or fellowship programme as an adjunct to specialty training.

Conclusions

Notwithstanding the limitations of a self‐reporting survey with a sub‐optimal response rate, there is significant demand for GH training and experiences among ACEM trainees. These findings should inform the development of safe and effective global emergency care training pathways, underpinned by mutually beneficial, international partnerships with educational and development objectives.
The handling oxygenation targets in the intensive care unit (HOT‐ICU) trial: Detailed statistical analysis plan
Authors: Schjørring Olav L. , Klitgaard Thomas L. , Perner Anders , Wetterslev Jørn , Lange Theis , Keus Frederik , Laake Jon H. , Morgan Matthew , Bäcklund Minna , Siegemund Martin , Thormar Katrin M. , Rasmussen Bodil S.
Published: February 2020

Background

No solid evidence exists on optimal oxygenation targets in intensive care patients. The handling oxygenation targets in the intensive care unit (HOT‐ICU) trial assesses the effects of a targeted arterial oxygen tension of 8 vs 12 kPa on 90‐day mortality in acutely admitted adult patients with hypoxaemic respiratory failure. This article describes the detailed statistical analysis plan for the predefined outcomes and supplementary analyses in the HOT‐ICU trial.

Methods

The trial will include 2928 patients to be able to detect or reject a true 20% relative risk reduction in the primary outcome of 90‐day all‐cause mortality with an α of 5% and a β of 10%. Analyses of the primary and secondary outcomes will be conducted according to the intention‐to‐treat principle and adjusted for stratification variables. The primary outcome and dichotomous secondary outcomes will be analysed using a generalised linear model with a log‐link and binomial error distribution. For the primary outcome, a 95% confidence interval (CI) not including 1.00 for the risk ratio will be considered statistically significant. Continuous secondary outcomes will be analysed using a generalised linear model or nonparametric test. CIs adjusted for the multiple secondary outcomes not including the null effect will be considered statistically significant. One planned interim analysis has been conducted.

Conclusions

The HOT‐ICU trial and the pre‐planned statistical analyses are designed to minimise bias and produce high quality data on the effects of a lower vs a higher oxygenation target throughout ICU admission in acutely admitted adult patients with hypoxaemic respiratory failure.

Registration

ClinicalTrials.gov identifier: NCT03174002, date of registration: June 2, 2017. European clinical trials database, EudraCT number 2017‐000632‐34.
Evidence of distinct gene functional patterns in GC‐poor and GC‐rich isochores in Bos taurus
Authors: Arhondakis S. , Milanesi M. , Castrignanò T. , Gioiosa S. , Valentini A. , Chillemi G.
Published: February 2020

Vertebrate genomes are mosaics of megabase‐size DNA segments with a fairly homogeneous base composition, called isochores. They are divided into five families characterized by different guanine‐cytosine (GC) levels and linked to several functional and structural properties. The increased availability of fully sequenced genomes allows the investigation of isochores in several species, assessing their level of conservation across vertebrate genomes. In this work, we characterized the isochores in Bos taurus using the ARS‐UCD1.2 genome version. The comparison of our results with the well‐studied human isochores and those of other mammals revealed a large conservation in isochore families, in number, average GC levels and gene density. Exceptions to the established increase in gene density with the increase in isochores (GC%) were observed for the following gene biotypes: tRNA, small nuclear RNA, small nucleolar RNA and pseudogenes that have their maximum number in H2 and H1 isochores. Subsequently, we assessed the ontology of all gene biotypes looking for functional classes that are statistically over‐ or under‐represented in each isochore. Receptor activity and sensory perception pathways were significantly over‐represented in L1 and L2 (GC‐poor) isochores. This was also validated for the horse genome. Our analysis of housekeeping genes confirmed a preferential localization in GC‐rich isochores, as reported in other species. Finally, we assessed the SNP distribution of a bovine high‐density SNP chip across the isochores, finding a higher density in the GC‐rich families, reflecting a potential bias in the chip, widely used for genetic selection and biodiversity studies.