bluuebunny/crossref_metadata_2025 huggingface dataset:
Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense
Authors: Chen Jian , Clinton Michael , Qi Guang , Wang Daowen , Liu Fengquan , Fu Zheng Qing
Published: February 2020

As a plant hormone, salicylic acid (SA) plays essential roles in plant defense against biotrophic and hemibiotrophic pathogens. Significant progress has been made in understanding the SA biosynthesis pathways and SA-mediated defense signaling networks in the past two decades. Plant defense responses involve rapid and massive transcriptional reprogramming upon the recognition of pathogens. Plant transcription factors and their co-regulators are critical players in establishing a transcription regulatory network and boosting plant immunity. A multitude of transcription factors and epigenetic regulators have been discovered, and their roles in SA-mediated defense responses have been reported. However, our understanding of plant transcriptional networks is still limited. As such, novel genomic tools and bioinformatic techniques will be necessary if we are to fully understand the mechanisms behind plant immunity. Here, we discuss current knowledge, provide an update on the SA biosynthesis pathway, and describe the transcriptional and epigenetic regulation of SA-mediated plant immune responses.
Foxtail mosaic virus-induced flowering assays in monocot crops
Authors: Yuan Chen , Li Hongmei , Qin Cheng , Zhang Xian , Chen Qianqian , Zhang Pengcheng , Xu Xiaorui , He Meiling , Zhang Xinlian , Tör Mahmut , Xue Dawei , Wang Huizhong , Jackson Stephen , He Yuehui , Liu Yule , Shi Nongnong , Hong Yiguo
Published: February 2020

Virus-induced flowering (VIF) exploits RNA or DNA viruses to express flowering time genes to induce flowering in plants. Such plant virus-based tools have recently attracted widespread attention for their fundamental and applied uses in flowering physiology and in accelerating breeding in dicotyledonous crops and woody fruit-trees. We now extend this technology to a monocot grass and a cereal crop. Using a Foxtail mosaic virus (FoMV)-based VIF system, dubbed FoMViF, we showed that expression of florigenic Flowering Locus T (FT) genes can promote early flowering and spikelet development in proso millet, a C4 grass species with potential as a nutritional food and biofuel resource, and in non-vernalized C3 wheat, a major food crop worldwide. Floral and spikelet/grain induction in the two monocot plants was caused by the virally expressed untagged or FLAG-tagged FT orthologs, and the florigenic activity of rice Hd3a was more pronounced than its dicotyledonous counterparts in proso millet. The FoMViF system is easy to use and its efficacy to induce flowering and early spikelet/grain production is high. In addition to proso millet and wheat, we envisage that FoMViF will be also applicable to many economically important monocotyledonous food and biofuel crops.
Plasma Sarcosine Measured by Gas Chromatography-Mass Spectrometry Distinguishes Prostatic Intraepithelial Neoplasia and Prostate Cancer from Benign Prostate Hyperplasia
Authors: Markin Pavel A , Brito Alex , Moskaleva Natalia , Fodor Miguel , Lartsova Ekaterina V , Shpot Yevgeny V , Lerner Yulia V , Mikhajlov Vasily Y , Potoldykova Natalia V , Enikeev Dimitry V , Lyundup Alexey V , Appolonova Svetlana A
Published: February 2020

Objective

Sarcosine was postulated in 2009 as a biomarker for prostate cancer (PCa). Here, we assess plasma sarcosine as a biomarker that is complementary to prostate-specific antigen (PSA).

Methods

Plasma sarcosine was measured using gas chromatography-mass spectrometry (GC-MS) in adults classified as noncancerous controls (with benign prostate hyperplasia [BPH], n = 36), with prostatic intraepithelial neoplasia (PIN, n = 16), or with PCa (n = 27). Diagnostic accuracy was assessed using receiver operating characteristic curve analysis.

Results

Plasma sarcosine levels were higher in the PCa (2.0 µM [1.3–3.3 µM], P <.01) and the PIN (1.9 µM [1.2–6.5 µM], P <.001) groups than in the BPH (0.9 µM [0.6–1.4 µM]) group. Plasma sarcosine had “good” and “very good” discriminative capability to detect PIN (area under the curve [AUC], 0.734) and PCa (AUC, 0.833) versus BPH, respectively. The use of PSA and sarcosine together improved the overall diagnostic accuracy to detect PIN and PCa versus BPH.

Conclusion

Plasma sarcosine measured by GC-MS had “good” and “very good” classification performance for distinguishing PIN and PCa, respectively, relative to noncancerous patients diagnosed with BPH.
Crystalline silicate absorption at 11.1 μm: ubiquitous and abundant in embedded YSOs and the interstellar medium
Authors: Do-Duy Tho , Wright Christopher M , Fujiyoshi Takuya , Glasse Alistair , Siebenmorgen Ralf , Smith Robert , Stecklum Bringfried , Sterzik Michael
Published: February 2020

Utilizing several instruments on 4–8 m telescopes, we have observed a large sample of objects in the mid-infrared (8–13 μm). These comprise a few evolved stars, multiple envelopes of embedded young stellar objects (YSOs) or compact H-II regions, and several sightlines through the interstellar medium (ISM). The latter is where dust resides – and is potentially modified – between its formation in evolved stellar outflows and deposition in molecular clouds. In most objects, we detect not only the well-known 9.7 μm absorption feature of amorphous silicates but also a second absorption band around 11.1 μm whose carrier is attributed to crystalline forsterite. We propose that crystalline silicates are essentially ubiquitous in the ISM and earliest phases of star formation, and are evolutionary precursors to T-Tauri and Herbig stars where such silicates have been commonly found. Modelling shows that in most YSOs, H-II regions and ISM cases, the forsterite mass fraction is between 1 and 2 per cent, suggesting that the younger phases inherit their abundance from the ISM. However, several sources show much stronger features (abundances ≥3 per cent). This suggests that significant processing, perhaps crystallization by thermal annealing, occurs early on in star formation. Most intriguing is the first detection of crystalline silicate in the diffuse ISM. We propose that our observed abundance is consistent with a mass fraction of crystalline silicates of 10–20 per cent injected into the ISM, along with commonly accepted lifetimes against their destruction, but only if cosmic ray-induced amorphization is insignificant over a few Giga years.
Comparative intranight optical variability of X-ray and γ-ray-detected narrow-line Seyfert 1 galaxies
Authors: Ojha Vineet , Chand Hum , Krishna Gopal , Mishra Sapna , Chand Krishan
Published: February 2020

In a systematic program to characterize the intranight optical variability (INOV) of different classes of narrow-line Seyfert 1 (NLSy1s) galaxies, we report here the first comparative INOV study of NLSy1 sets detected in the X-ray and γ-ray bands. Our sample consists of 18 sources detected in X-rays but not in γ-rays (hereafter x_NLSy1s) and seven sources detected in γ-rays (hereafter g_NLSy1s), out of which five are detected also in X-rays. We have monitored these two sets of NLSy1s, respectively, in 24 and 21 sessions of a minimum of 3-h duration each. The INOV duty cycles for these two sets are found to be 12 per cent and 53 per cent, respectively (at a 99 per cent confidence level). In the set of 18 x_NLSy1s, INOV duty cycle is found to be zero for the 13 radio-quiet members (monitored in 14 sessions) and 43 per cent for the five radio-loud members (10 sessions). The latter is very similar to the aforementioned duty cycle of 53 per cent found here for the set of g_NLSy1s (all of which are radio-loud). Thus, it appears that the radio-loudness level is the prime factor behind the INOV detection and the pattern of the high-energy radiation plays only a minor role.
Deep multiredshift limits on Epoch of Reionization 21 cm power spectra from four seasons of Murchison Widefield Array observations
Authors: Trott Cathryn M , Jordan C H , Midgley S , Barry N , Greig B , Pindor B , Cook J H , Sleap G , Tingay S J , Ung D , Hancock P , Williams A , Bowman J , Byrne R , Chokshi A , Hazelton B J , Hasegawa K , Jacobs D , Joseph R C , Li W , Line J L B , Lynch C , McKinley B , Mitchell D A , Morales M F , Ouchi M , Pober J C , Rahimi M , Takahashi K , Wayth R B , Webster R L , Wilensky M , Wyithe J S B , Yoshiura S , Zhang Z , Zheng Q
Published: February 2020

We compute the spherically averaged power spectrum from four seasons of data obtained for the Epoch of Reionization (EoR) project observed with the Murchison Widefield Array (MWA). We measure the EoR power spectrum over k = 0.07–3.0 h Mpc−1 at redshifts $z$ = 6.5–8.7. The largest aggregation of 110 h on EoR0 high band (3340 observations), yields a lowest measurement of (43 mK)2 = 1.8 × 103 mK2 at k  = 0.14 h Mpc−1 and $z$ = 6.5 (2σ thermal noise plus sample variance). Using the Real-Time System to calibrate and the CHIPS pipeline to estimate power spectra, we select the best observations from the central five pointings within the 2013–2016 observing seasons, observing three independent fields and in two frequency bands. This yields 13 591 2-min snapshots (453 h), based on a quality assurance metric that measures ionospheric activity. We perform another cut to remove poorly calibrated data, based on power in the foreground-dominated and EoR-dominated regions of the two-dimensional power spectrum, reducing the set to 12 569 observations (419 h). These data are processed in groups of 20 observations, to retain the capacity to identify poor data, and used to analyse the evolution and structure of the data over field, frequency, and data quality. We subsequently choose the cleanest 8935 observations (298 h of data) to form integrated power spectra over the different fields, pointings, and redshift ranges.
Analytical model for cluster radio relics
Authors: Brüggen M , Vazza F
Published: February 2020

Radio relics are vast synchrotron sources that sit on the outskirts of merging galaxy clusters. In this work we model their formation using a Press–Schechter formalism to simulate merger rates, analytical models for the intracluster medium and the shock dynamics, as well as a simple model for the cosmic ray electrons at the merger shocks. We show that the statistical properties of the population of radio relics are strongly dependent on key physical parameters, such as the acceleration efficiency, the magnetic field strength at the relic, the geometry of the relic and the duration of the electron acceleration at merger shocks. It turns out that the flux distribution as well as the power–mass relation can constrain key parameters of the intracluster medium. With the advent of new large-area radio surveys, statistical analyses of radio relics will complement what we have learned from observations of individual objects.
Reflex motion in the Milky Way stellar halo resulting from the Large Magellanic Cloud infall
Authors: Petersen Michael S , Peñarrubia Jorge
Published: February 2020

We present the results of N-body models of the Milky Way and Large Magellanic Cloud system and study the kinematic reflex motion in the stellar halo owing to the barycentre displacement of the disc. In agreement with previous studies, we find that the Milky Way disc may be moving at 40 $\, {\rm km~s^{-1}}$ relative to the barycentre prior to the Large Magellanic Cloud infall. The resulting reflex motion is visible in tangential velocities of the stellar halo as a simple dipole. The signal is strongest for stars with long dynamical times, identifiable in position-velocity data as stars with large apocentres, whose dynamical memory is still well represented by the unperturbed Milky Way potential. The signal varies across the sky depending on the stellar tracer and may be up to the same magnitude as the velocity of the disc centre of mass, making reflex motion a source of bias for Milky Way potential determinations based on the modelling of stellar streams and/or smooth halo tracers such as blue horizontal branch or RR Lyrae stars.
Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas
Authors: Gouveia Mateus H , Borda Victor , Leal Thiago P , Moreira Rennan G , Bergen Andrew W , Kehdy Fernanda S G , Alvim Isabela , Aquino Marla M , Araujo Gilderlanio S , Araujo Nathalia M , Furlan Vinicius , Liboredo Raquel , Machado Moara , Magalhaes Wagner C S , Michelin Lucas A , Rodrigues Maíra R , Rodrigues-Soares Fernanda , Sant Anna Hanaisa P , Santolalla Meddly L , Scliar Marília O , Soares-Souza Giordano , Zamudio Roxana , Zolini Camila , Bortolini Maria Catira , Dean Michael , Gilman Robert H , Guio Heinner , Rocha Jorge , Pereira Alexandre C , Barreto Mauricio L , Horta Bernardo L , Lima-Costa Maria F , Mbulaiteye Sam M , Chanock Stephen J , Tishkoff Sarah A , Yeager Meredith , Tarazona-Santos Eduardo
Published: February 2020

The Transatlantic Slave Trade transported more than 9 million Africans to the Americas between the early 16th and the mid-19th centuries. We performed a genome-wide analysis using 6,267 individuals from 25 populations to infer how different African groups contributed to North-, South-American, and Caribbean populations, in the context of geographic and geopolitical factors, and compared genetic data with demographic history records of the Transatlantic Slave Trade. We observed that West-Central Africa and Western Africa-associated ancestry clusters are more prevalent in northern latitudes of the Americas, whereas the South/East Africa-associated ancestry cluster is more prevalent in southern latitudes of the Americas. This pattern results from geographic and geopolitical factors leading to population differentiation. However, there is a substantial decrease in the between-population differentiation of the African gene pool within the Americas, when compared with the regions of origin from Africa, underscoring the importance of historical factors favoring admixture between individuals with different African origins in the New World. This between-population homogenization in the Americas is consistent with the excess of West-Central Africa ancestry (the most prevalent in the Americas) in the United States and Southeast-Brazil, with respect to historical-demography expectations. We also inferred that in most of the Americas, intercontinental admixture intensification occurred between 1750 and 1850, which correlates strongly with the peak of arrivals from Africa. This study contributes with a population genetics perspective to the ongoing social, cultural, and political debate regarding ancestry, admixture, and the mestizaje process in the Americas.
TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data
Authors: Goubert Clément , Thomas Jainy , Payer Lindsay M , Kidd Jeffrey M , Feusier Julie , Watkins W Scott , Burns Kathleen H , Jorde Lynn B , Feschotte Cédric
Published: February 2020

Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alus are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alus and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline – TypeTE – which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a high-quality set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.
Optimization via game theoretic control
Authors: Cheng Daizhan , Liu Zequn
Published: February 2020

Using game theoretic control to solve optimization problem is a recently developed promising method. The key technique is to convert a networked system into a potential game, with a pre-assigned criterion as the potential function. An algorithm is designed for updating strategies to reach a Nash equilibrium (i.e. optimal solution).
Nutritional interventions to improve muscle mass, muscle strength, and physical performance in older people: an umbrella review of systematic reviews and meta-analyses
Authors: Gielen Evelien , Beckwée David , Delaere Andreas , De Breucker Sandra , Vandewoude Maurits , Bautmans Ivan ,   the Sarcopenia Guidelines Development Group of the Belgian Society of Gerontology and Geriatrics (BSGG), Bautmans I , Beaudart C , Beckwée D , Beyer I , Bruyère O , De Breucker S , De Cock A.-M. , Delaere A , de Saint-Hubert M , De Spiegeleer A , Gielen E , Perkisas S , Vandewoude M
Published: February 2020

Context

Sarcopenia is a progressive and generalized skeletal muscle disorder associated with an increased risk of adverse outcomes such as falls, disability, and death. The Belgian Society of Gerontology and Geriatrics has developed evidence-based guidelines for the prevention and treatment of sarcopenia. This umbrella review presents the results of the Working Group on Nutritional Interventions.

Objective

The aim of this umbrella review was to provide an evidence-based overview of nutritional interventions targeting sarcopenia or at least 1 of the 3 sarcopenia criteria (ie, muscle mass, muscle strength, or physical performance) in persons aged ≥ 65 years.

Data sources

Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, the PubMed and Web of Science databases were searched for systematic reviews and meta-analyses reporting the effect of nutritional supplementation on sarcopenia or muscle mass, strength, or physical performance.

Data extraction

Two authors extracted data on the key characteristics of the reviews, including participants, treatment, and outcomes. Methodological quality of the reviews was assessed using the product A Measurement Tool to Assess Systematic Reviews. Three authors synthesized the extracted data and generated recommendations on the basis of an overall synthesis of the effects of each intervention. Quality of evidence was rated with the Grading of Recommendations Assessment, Development and Evaluation approach.

Data analysis

A total of 15 systematic reviews were included. The following supplements were examined: proteins, essential amino acids, leucine, β-hydroxy-β-methylbutyrate, creatine, and multinutrient supplementation (with or without physical exercise). Because of both the low amount and the low to moderate quality of the reviews, the level of evidence supporting most recommendations was low to moderate.

Conclusions

Best evidence is available to recommend leucine, because it has a significant effect on muscle mass in elderly people with sarcopenia. Protein supplementation on top of resistance training is recommended to increase muscle mass and strength, in particular for obese persons and for ≥ 24 weeks. Effects on sarcopenia as a construct were not reported in the included reviews.
Galactolipid DGDG and Betaine Lipid DGTS Direct De Novo Synthesized Linolenate into Triacylglycerol in a Stress-Induced Starchless Mutant of Chlamydomonas reinhardtii
Authors: Yang Miao , Kong Fantao , Xie Xi , Wu Peichun , Chu Yadong , Cao Xupeng , Xue Song
Published: February 2020

The increasing demand for triacylglycerol (TAG) enriching polyunsaturated fatty acids (PUFAs) has led to a surge of interest in microalgal TAG metabolism. Polar membrane lipids serve as the desaturation carrier for PUFA, and the functional group of PUFA can be incorporated into TAG. Monogalactoglycerolipid has been found to provide the de novo synthesized oleate acyl group or the nascent polyunsaturated diacylglycerol backbone for TAG biosynthesis in the model green alga, Chlamydomonas reinhardtii. However, whether other membrane lipids take part in the formation of PUFA-attached TAG has not been clearly discovered. A time course study of glycerolipidomics in the starchless mutant of C. reinhardtii, BAFJ5, which hyper-accumulates TAG, revealed that digalactosyldiacylglycerol (DGDG) and diacylglycerol-N,N,N-trimethylhomoserine (DGTS) turned into the main components of membrane lipids, accounting for 62% of the total polar lipids, under nitrogen deprivation combined with high light conditions. In addition, the membrane lipid molecules DGDG 18:3n3/16:0 and DGTS 16:0/18:3n6 were presumed to be involved in the consecutive integration of the de novo synthesized linolenates into TAG. Based on the stoichiometry calculation, DGDG and DGTS were demonstrated to provide a major contribution to the accumulation of linolenate-attached TAG. Our study gives insights into the potential PUFA-attached TAG formation pathway mediated by the turnover of de novo synthesized DGDG and DGTS in the starchless mutant of Chlamydomonas.
SlSNAT Interacts with HSP40, a Molecular Chaperone, to Regulate Melatonin Biosynthesis and Promote Thermotolerance in Tomato
Authors: Wang Xiaoyun , Zhang Haijun , Xie Qian , Liu Ying , Lv Hongmei , Bai Ruyue , Ma Rui , Li Xiangdong , Zhang Xichun , Guo Yang-Dong , Zhang Na
Published: February 2020

The SNAT enzyme participates in the biosynthesis of melatonin, which is reported to regulate thermotolerance in many plants. However, the mechanistic basis of this regulation remains unclear. In this study, we identified the SlSNAT gene, which is responsible for melatonin biosynthesis in tomato. SlSNAT expression levels were 3- and 5-fold higher in SlSNAT overexpression lines OX-2 and OX-6, respectively. The melatonin levels were 3- and 4-fold higher than those in wild type. The melatonin levels decreased by 50% when the expression of SlSNAT was downregulated to 40%. Overexpression of SlSNAT in tomato plants provided significantly enhanced thermotolerance with better growth performance in Photosystem II (PSII) maximum photochemical quantum yield (Fv/Fm) and alleviated heat injury. Both exogenous melatonin treatment and endogenous melatonin manipulation by SlSNAT overexpression decreased the levels of reactive oxygen species�accumulation and Fv/Fm. The SlSNAT overexpression line showed protected ribulose bisphosphate carboxylase oxygenase proteins and upregulated response of heat transcription factors and heat shock proteins under heat stress. HSP40, a DnaJ-type chaperone, was found to interact with SlSNAT in the chloroplast. Downregulation of HSP40 showed lower melatonin synthesis under heat stress. HSP40 functions as a chaperone to protect the SNAT enzyme during melatonin synthesis under heat stress. HSP40 interacted with SlSNAT and together participated in melatonin-related thermotolerance regulation in tomato.
Negative associations for fasting blood glucose, cholesterol and triglyceride levels with the development of giant cell arteritis
Authors: Wadström Karin , Jacobsson Lennart , Mohammad Aladdin J , Warrington Kenneth J , Matteson Eric L , Turesson Carl
Published: February 2020

Objectives

To investigate metabolic features that may predispose to GCA in a nested case–control study.

Methods

Individuals who developed GCA after inclusion in a population-based health survey (the Malmö Preventive Medicine Project; N = 33 346) were identified and validated through a structured review of medical records. Four controls for every validated case were selected from the database.

Results

A total of 76 cases with a confirmed incident diagnosis of GCA (61% female, 65% biopsy positive, mean age at diagnosis 70 years) were identified. The median time from screening to diagnosis was 20.7 years (range 3.0–32.1). Cases had significantly lower fasting blood glucose (FBG) at baseline screening compared with controls [mean 4.7 vs 5.1 mmol/l (S.d. overall 1.5), odds ratio (OR) 0.35 per mmol/l (95% CI 0.17, 0.71)] and the association remained significant when adjusted for smoking [OR 0.33 per mmol/l (95% CI 0.16, 0.68)]. Current smokers had a reduced risk of GCA [OR 0.35 (95% CI 0.18, 0.70)]. Both cholesterol [mean 5.6 vs 6.0 mmol/l (S.d. overall 1.0)] and triglyceride levels [median 1.0 vs 1.2 mmol/l (S.d. overall 0.8)] were lower among the cases at baseline screening, with significant negative associations with subsequent GCA in crude and smoking-adjusted models [OR 0.62 per mmol/l (95% CI 0.43, 0.90) for cholesterol; 0.46 per mmol/l (95% CI 0.27, 0.81) for triglycerides].

Conclusion

Development of GCA was associated with lower FBG and lower cholesterol and triglyceride levels at baseline, all adjusted for current smoking, suggesting that metabolic features predispose to GCA.
Prism Adaptation Deficits in Schizophrenia
Authors: Bartolomeo Lisa A , Shin Yong-Wook , Block Hannah J , Bolbecker Amanda R , Breier Alan F , O’Donnell Brian , Hetrick William P
Published: February 2020

Recent clinical and neurobehavioral evidence suggests cerebellar dysfunction in schizophrenia (SZ). We used the prism adaptation motor task (PAT) to probe specific cerebellar circuits in the disorder. PAT requires cerebellum-dependent motor adaptation, perceptual remapping, and strategic control. A failure to engage in early corrective processes may indicate impairment within either the cerebellum or regions contributing to strategic components, such as the parietal lobe, while an inability to develop and retain a visuomotor shift with time strongly suggests cerebellar impairment. Thirty-one individuals with SZ and 31 individuals without a history of psychological disorders completed PAT. Subjects reached to a target before, during, and following prism exposure, while their movements were recorded using motion-sensing technology. The SZ group performed worse on conditions consisting of adaptation, post-adaptation, aftereffects, and reorientation, thereby demonstrating a failure to adapt to the same degree as healthy controls. SZ performance remained impaired even with visual feedback and did not differ from controls at baseline, suggesting the observed deficit is specific to adaptation. Results indicate that sensorimotor adaptation is impaired in SZ and implicate disturbances in cerebellar circuits.
Investigating the WHAT and WHY on older adults’ use of neighborhood open spaces following an environmental intervention
Authors: Schmidt Tanja , Pawlowski Charlotte Skau , Kerr Jacqueline , Schipperijn Jasper
Published: February 2020

Using neighborhood open spaces (NOS) may be an easy way for older adults to maintain healthy aging through physical activity and social interaction. Little is known about older adults’ use of NOS, their preferences, and barriers to using them. This paper presents older adults’ use of NOS in a deprived neighborhood before and after an intervention and factors promoting or inhibiting their use using convergent mixed methods design. Participatory research was employed involving older adults in the intervention. The System for Observing Play and Recreation in Communities was used to observe older adults’ use of 13 NOS in spring 2017 (baseline) and spring 2018 (follow-up). Ten interviews were conducted in 2018 to identify barriers and facilitators for using NOS. Two NOS had a pavilion built and, in one NOS, benches were renovated, including building raised flower beds and small tables. At baseline, 209 older adults were observed, whereas 329 were observed at follow-up. More (44%) older adults were observed at follow-up in the NOS with the renovated benches. No use of the two pavilions was observed. The interviews identified six factors important for older adults’ use of NOS: weather, support for social caretakers, support for resourceful volunteers, organized activities, social interaction, and sense of ownership. Organizational resources, such as social caretakers and volunteers, are important to promote older adults’ use of NOS. Social interaction is a key factor for older adults’ use of NOS and should be prioritized by health promoters.
What Drives Successful Economic Diversification in Resource-Rich Countries?
Authors: Lashitew Addisu A , Ross Michael L , Werker Eric
Published: February 2020

The “resource curse” is often understood to imply poor growth in the non-resource sectors of the economy, but research into the diversification performance of resource-rich countries is limited. This paper surveys recent evidence and identifies empirical patterns in the economic diversification of resource-rich countries. Diversification is measured using the growth of per capita non-resource (manufacturing and services) sectors in domestic and export markets, which has a cleaner interpretation than competing measures. This measure is used to evaluate the long-term diversification of countries that started off as resource-dependent, and to rank countries according to their performance. We then identify policy-relevant correlates of diversification at the national level, including the acquisition of human capital, public and intellectual capital, and firm dynamism. More resource-dependent countries appear to perform worse on measures of human capital and intellectual capital, but more resource-abundant countries perform better on public capital and human capital accumulation. We examine the mechanisms behind diversification performance through in-depth case studies of Oman, Laos, and Indonesia, and conclude by identifying policy lessons and future research directions.
Molecular characterization of the first reported Aichivirus A in Australia
Authors: Northill Judith A. , Simmons Russell J. , Genge Doris , Moore Frederick A.
Published: February 2020

A novel real-time reverse transcription polymerase chain reaction (RT-rPCR) assay was developed to detect Aichivirus A (AiV-A) based on four complete genomes. The assay successfully detected AiV-A in a sample from a patient with acute gastroenteritis in January 2008. Screening of 756 samples submitted for norovirus testing during May 2008 detected a further 23 AiV-A-positive samples from 18 individual patients. Genotyping using novel primers targeting the 3C–3D junction region identified AiV-A genotype B. Further sequencing of the VP1 region supported the 3C–3D result. All three assays proved useful to support foodborne outbreak investigations. This is the first report of AiV-A detection in Australia.
Insights into plant-beneficial traits of probiotic Pseudomonas chlororaphis isolates
Authors: Anderson Anne J. , Kim Young Cheol
Published: February 2020

Pseudomonas chlororaphisisolates have been studied intensively for their beneficial traits.P. chlororaphisspecies function as probiotics in plants and fish, offering plants protection against microbes, nematodes and insects. In this review, we discuss the classification ofP. chlororaphisisolates within four subspecies; the shared traits include the production of coloured antimicrobial phenazines, high sequence identity between housekeeping genes and similar cellular fatty acid composition. The direct antimicrobial, insecticidal and nematocidal effects ofP. chlororaphisisolates are correlated with known metabolites. Other metabolites prime the plants for stress tolerance and participate in microbial cell signalling events and biofilm formation among other things. Formulations ofP. chlororaphisisolates and their metabolites are currently being commercialized for agricultural use.
Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-19)
Authors: Nishiura Hiroshi , Kobayashi Tetsuro , Miyama Takeshi , Suzuki Ayako , Jung Sung-mok , Hayashi Katsuma , Kinoshita Ryo , Yang Yichi , Yuan Baoyin , Akhmetzhanov Andrei R. , Linton Natalie M.
Published: February 2020

A total of 565 Japanese citizens were evacuated from Wuhan, China to Japan. All passengers were screened for symptoms and also undertook reverse transcription polymerase chain reaction testing, identifying 5 asymptomatic and 7 symptomatic passengers testing positive for 2019-nCoV. We show that the screening result is suggestive of the asymptomatic ratio at 41.6%.
Bulk and single-cell transcriptomics identify tobacco-use disparity in lung gene expression of ACE2, the receptor of 2019-nCov
Authors: Cai Guoshuai
Published: February 2020

In current severe global emergency situation of 2019-nCov outbreak, it is imperative to identify vulnerable and susceptible groups for effective protection and care. Recently, studies found that 2019-nCov and SARS-nCov share the same receptor, ACE2. In this study, we analyzed five large-scale bulk transcriptomic datasets of normal lung tissue and two single-cell transcriptomic datasets to investigate the disparities related to race, age, gender and smoking status in ACE2 gene expression and its distribution among cell types. We didn’t find significant disparities in ACE2 gene expression between racial groups (Asian vs Caucasian), age groups (>60 vs <60) or gender groups (male vs female). However, we observed significantly higher ACE2 gene expression in former smoker’s lung compared to non-smoker’s lung. Also, we found higher ACE2 gene expression in Asian current smokers compared to non-smokers but not in Caucasian current smokers, which may indicate an existence of gene-smoking interaction. In addition, we found that ACE2 gene is expressed in specific cell types related to smoking history and location. In bronchial epithelium, ACE2 is actively expressed in goblet cells of current smokers and club cells of non-smokers. In alveoli, ACE2 is actively expressed in remodelled AT2 cells of former smokers. Together, this study indicates that smokers especially former smokers may be more susceptible to 2019-nCov and have infection paths different with non-smokers. Thus, smoking history may provide valuable information in identifying susceptible population and standardizing treatment regimen.
Reported autism diagnosis strongly predicts psychotic-like experiences in the Adolescent Brain Cognitive Development cohort
Authors: Jutla Amandeep , Donohue Meghan Rose , Veenstra-VanderWeele Jeremy , Foss-Feig Jennifer H.
Published: February 2020

Although the schizophrenia rate is increased in autism spectrum disorder (ASD), it is difficult to identify which youth with ASD will go on to develop psychosis. We explored the relationship between ASD and emerging psychotic-like experiences in the Adolescent Brain Cognitive Development (ABCD) cohort of school-aged children. We predicted that ASD would robustly predict psychotic-like experience severity, even relative to other established predictors, and that ASD youth with psychotic-like experiences would have a characteristic neurocognitive profile. In a sample of 9,130 youth aged 9–11, we fit regression models that included parent-reported ASD, family history of psychosis, lifetime trauma, executive function, processing speed, working memory, age, sex, race, ethnicity, and income-to-needs ratio as predictors of Prodromal Questionnaire – Brief Child (PQ-BC) score. We assessed cognitive profiles using analysis of variance on NIH Toolbox measures. ASD increased PQ-BC distress scores by 2.46 points (95% CI 1.32 – 3.60), an effect at least as large as those of family history of psychosis (1.05 points, 95% CI 0.56 – 1.53), Latinx ethnicity (0.99 points, 95% CI 0.52 – 1.45) and black race (0.89 points, 95% CI 0.30 – 1.48). We did not identify a unique cognitive profile for ASD youth with psychotic-like experiences. Our finding that ASD predicts psychotic-like symptoms in youth is consistent with previous literature, and adds new information in suggesting that ASD is a strong predictor of psychotic-like experiences even when compared to other established SCZ risk factors.
Transmission Dynamics of COVID-19 in Malaysia Prior to the Movement Control Order
Authors: Labadin J , Hong B.H
Published: February 2020

This paper focuses on the formulation of a deterministic COVID-19 transmission model by considering the exposed and recovered populations with immunity. The scenario of the simulation is depicted based on the patient zero in Malaysia. The transmission model is found to be able to predict the next confirmed case given a single case is introduced in a fully susceptible population. The mathematical model is developed based on the SEIR model which has susceptible, exposed, infectious and recovered populations. The system of equations which were obtained were solved numerically and the simulation results were analyzed. The analysis includes the impact of the disease if no control is taken.
Circular RNA and its mechanisms in diabetic retinopathy: a systematic review
Authors: He Miao , Zhou Rouxi , Liu Sen , Cheng Weijing , Wang Wei
Published: February 2020

Circular RNAs (CircRNAs) are endogenous long non-coding RNAs. Unlike linear RNAs, they are structurally continuous and covalently closed, without 5 ’caps or 3’ polyadenylation tails. High-throughput RNA sequencing has enabled people to find several endogenous circRNAs in different species and tissues. circRNA mainly acts as a sponge for microRNAs in cytoplasm to regulates protein translation, or interacts with RNA-binding proteins to generate RNA protein complexes that control transcription. circRNAs are closely associated with diseases such as diabetes, neurological disorders, cardiovascular diseases and cancer, which indicates that circRNAs are closely related to and also play an important functional role in the occurrence and development of human diseases. Recent studies have shown that they are differentially expressed in healthy and diseased eye tissues. There lacks of biomarkers for early detection of diabetic retinopathy, and the newly discovered circRNAs seem to be an ideal candidate of novel molecular markers and therapeutic targets. However, the molecular mechanism of circRNAs activity in the occurrence and development of diabetic retinopathy are not clear yet. This systematic review aims to summarize the research status on function and mechanism of circRNAs in regulating the occurrence of diabetic retinopathy.
CAR T cells for solid tumors: genome-wide dysfunction signature confirms value of c-Jun overexpression, but signals heterogeneity
Authors: Benhenda Mostapha
Published: February 2020

Chimeric antigen receptor (CAR) T cells still have limited effects in cancer, and especially in solid tumors, due to T cell dysfunction and exhaustion. CAR T cells overexpressing c-Jun (JUN CAR T cells) have been introduced to solve this problem. In this paper, we analyze JUN CAR T cells scRNA-seq data in solid tumors, by applying a genome-wide signature of T cell dysfunction, TID. This signature comes from the bulk RNA-seq signature TIDE, introduced to predict immune checkpoint inhibitor response. Our analysis confirms that on average, JUN CAR T cells are less dysfunctional than non-JUN CAR T cells. However, it also shows heterogeneity within JUN CAR T cells, which brings uncertainty about possible tumor resistance. We conclude that genome-wide dysfunction signature TID helps de-risking CAR T cell therapy for solid tumors.
Estimation of the Time-Varying Reproduction Number of COVID-19 Outbreak in China
Authors: You Chong , Deng Yuhao , Hu Wenjie , Sun Jiarui , Lin Qiushi , Zhou Feng , Pang Cheng Heng , Zhang Yuan , Chen Zhengchao , Zhou Xiao-Hua
Published: February 2020

Background

The 2019-nCoV outbreak in Wuhan, China has attracted world-wide attention. As of February 11, 2020, a total of 44730 cases of novel coronavirus-infected pneumonia associated with COVID-19 were confirmed by the National Health Commission of China.

Methods

Three approaches, namely Poisson likelihood-based method (ML), exponential growth rate-based method (EGR) and stochastic Susceptible-Infected-Removed dynamic model-based method (SIR), were implemented to estimate the basic and controlled reproduction numbers.

Results

A total of 71 chains of transmission together with dates of symptoms onset and 67 dates of infections were identified among 5405 confirmed cases outside Hubei as reported by February 2, 2020. Based on this information, we find the serial interval having an average of 4.41 days with a standard deviation of 3.17 days and the infectious period having an average of 10.91 days with a standard deviation of 3.95 days.

Conclusions

The controlled reproduction number is declining. It is lower than one in most regions of China, but is still larger than one in Hubei Province. Sustained efforts are needed to further reduce the Rc to below one in order to end the current epidemic.
Assessing the plausibility of supercritical transmission for an emerging or re-emerging pathogen
Authors: Blumberg Seth , Lu Phoebe , Lietman Thomas M , Porco Travis C
Published: February 2020

Rapid assessment of the transmission potential of an emerging or reemerging pathogen is a cornerstone of public health response. A simple approach is shown for using the number of disease introductions and secondary cases to determine whether the upper bound of the reproduction number exceeds the critical value of one.
RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
Authors: de la Rubia Ivan , Srivastava Akanksha , Xue Wenjing , Indi Joel A , Carbonell-Sala Silvia , Lagarde Julien , Albà M Mar , Eyras Eduardo
Published: February 2020

Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes from any sample. However, current methods for transcript identification and quantification rely of mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. Here we present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts. RATTLE provides unprecedented access to transcriptomes from any sample and species without relying on a reference or additional technologies.
The effect of travel restrictions on the spread of the 2019 novel coronavirus (2019-nCoV) outbreak
Authors: Chinazzi Matteo , Davis Jessica T. , Ajelli Marco , Gioannini Corrado , Litvinova Maria , Merler Stefano , y Piontti Ana Pastore , Rossi Luca , Sun Kaiyuan , Viboud Cécile , Xiong Xinyue , Yu Hongjie , Halloran M. Elizabeth , Longini Ira M. , Vespignani Alessandro
Published: February 2020

Motivated by the rapid spread of a novel coronavirus (2019-nCoV) in Mainland China, we use a global metapopulation disease transmission model to project the impact of both domestic and international travel limitations on the national and international spread of the epidemic. The model is calibrated on the evidence of internationally imported cases before the implementation of the travel quarantine of Wuhan. By assuming a generation time of 7.5 days, the reproduction number is estimated to be 2.4 [90% CI 2.2-2.6]. The median estimate for number of cases before the travel ban implementation on January 23, 2020 is 58,956 [90% CI 40,759 - 87,471] in Wuhan and 3,491 [90% CI 1,924 - 7,360] in other locations in Mainland China. The model shows that as of January 23, most Chinese cities had already received a considerable number of infected cases, and the travel quarantine delays the overall epidemic progression by only 3 to 5 days. The travel quarantine has a more marked effect at the international scale, where we estimate the number of case importations to be reduced by 80% until the end of February. Modeling results also indicate that sustained 90% travel restrictions to and from Mainland China only modestly affect the epidemic trajectory unless combined with a 50% or higher reduction of transmission in the community.
Assessing the Tendency of 2019-nCoV (COVID-19) Outbreak in China
Authors: Liu Qinghe , Liu Zhicheng , Li Deqiang , Gao Zefei , Zhu Junkai , Yang Junyan , Wang Qiao
Published: February 2020

Since December 1, 2019, the spread of COVID-19 is increasing every day. It is particularly important to predict the trend of the epidemic for the timely adjustment of the economy and industries. We proposed a Flow-SEHIR model in this paper to perform the trends of 2019-nCoV (COVID-19) in China.

The results show that the number of daily confirmed new cases reaches the inflection point on Feb. 6 – 10 outside Hubei. For the maximum of temporal infected cases number, the predicted peak value in China except Hubei was estimated to be 21721 (95% CI: 18764 - 24929). The peak arrival time is on March 3 - 9. The temporal number of patients in most areas of China outside Hubei will peak from March 12 to March 15. The peak values of more than 73.5% provinces or regions in China will be controlled within 1000. According to Flow-SEHIR model and estimations from the data of evacuation of nationals from Wuhan, the real peak cumulative number of patients in Hubei is estimated to be 403481 (95% CI: 143284 – 1166936).
Both DNA binding domains of p53 are required for its ultra-rapid recruitment to sites of UV damage
Authors: Wang YH. , Ho T. , Hariharan A. , Goh HC. , Sheetz MP. , Lane DP.
Published: February 2020

p53 concentrates at DNA damage sites within two seconds upon UV laser micro-irradiation. Structural analysis shows that this very rapid response requires both the DNA binding and C-terminal domains of p53. This early recruitment response is also PARP-dependent. As mutations within the DNA binding domain of p53, that are commonly associated with cancer also inhibit this rapid binding, we suggest that this is an important initial step for p53 function as a tumor suppressor.

One Sentence Summary

p53 is an early responder to DNA damage