bluuebunny/crossref_metadata_2025 huggingface dataset:
An in-depth investigation of 11 pulsars discovered by FAST
Authors: Cameron A D , Li D , Hobbs G , Zhang L , Miao C C , Wang J B , Yuan M , Wang S , Jacobs Corban G , Cruces M , Dai S , Feng Y , Han J , Kaczmarek J F , Niu J R , Pan Z C , Qian L , Tao Z Z , Wang P , Wang S Q , Xu H , Xu R X , Yue Y L , Zhang S B , Zhi Q J , Zhu W W , Champion D J , Kramer M , Zhou S Q , Qiu K P , Zhu M
Published: May 2020

We present timing solutions and analyses of 11 pulsars discovered by the Five-hundred-meter Aperture Spherical radio Telescope (FAST). These pulsars were discovered using an ultrawide bandwidth receiver in drift-scan observations made during the commissioning phase of FAST, and were then confirmed and timed using the 64-m Parkes Radio Telescope. Each pulsar has been observed over a span of at least one year. Highlighted discoveries include PSR J0344−0901, which displays mode-changing behaviour and may belong to the class of so-called swooshing pulsars (alongside PSRs B0919+06 and B1859+07); PSR J0803−0942, whose emission is almost completely linearly polarized; and PSRs J1900−0134 and J1945+1211, whose well-defined polarization angle curves place stringent constraints on their emission geometry. We further discuss the detectability of these pulsars by earlier surveys, and highlight lessons learned from our work in carrying out confirmation and monitoring observations of pulsars discovered by a highly sensitive telescope, many of which may be applicable to next-generation pulsar surveys. This paper marks one of the first major releases of FAST-discovered pulsars, and paves the way for future discoveries anticipated from the Commensal Radio Astronomy FAST Survey.
Asteroseismology of 36 Kepler subgiants – I. Oscillation frequencies, linewidths, and amplitudes
Authors: Li Yaguang , Bedding Timothy R , Li Tanda , Bi Shaolan , Stello Dennis , Zhou Yixiao , White Timothy R
Published: May 2020

The presence of mixed modes makes subgiants excellent targets for asteroseismology, providing a probe for the internal structure of stars. Here we study 36 Kepler subgiants with solar-like oscillations and report their oscillation mode parameters. We performed a so-called peakbagging exercise, i.e. estimating oscillation mode frequencies, linewidths, and amplitudes with a power spectrum model, fitted in the Bayesian framework and sampled with a Markov chain Monte Carlo algorithm. The uncertainties of the mode frequencies have a median value of 0.180 μHz. We obtained seismic parameters from the peakbagging, analysed their correlation with stellar parameters, and examined against scaling relations. The behaviour of seismic parameters (e.g. Δν, νmax, ϵp) is in general consistent with theoretical predictions. We presented the observational p–g diagrams, namely γ1–Δν for early subgiants and ΔΠ1–Δν for late subgiants, and demonstrate their capability to estimate stellar mass. We also found a log g dependence on the linewidths and a mass dependence on the oscillation amplitudes and the widths of oscillation excess. This sample will be valuable constraints for modelling stars and studying mode physics such as excitation and damping.
OzDES multi-object fibre spectroscopy for the Dark Energy Survey: results and second data release
Authors: Lidman C , Tucker B E , Davis T M , Uddin S A , Asorey J , Bolejko K , Brout D , Calcino J , Carollo D , Carr A , Childress M , Hoormann J K , Foley R J , Galbany L , Glazebrook K , Hinton S R , Kessler R , Kim A G , King A , Kremin A , Kuehn K , Lagattuta D , Lewis G F , Macaulay E , Malik U , March M , Martini P , Möller A , Mudd D , Nichol R C , Panther F , Parkinson D , Pursiainen M , Sako M , Swann E , Scalzo R , Scolnic D , Sharp R , Smith M , Sommer N E , Sullivan M , Webb S , Wiseman P , Yu Z , Yuan F , Zhang B , Abbott T M C , Aguena M , Allam S , Annis J , Avila S , Bertin E , Bhargava S , Brooks D , Carnero Rosell A , Carrasco Kind M , Carretero J , Castander F J , Costanzi M , da Costa L N , De Vicente J , Doel P , Eifler T F , Everett S , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hartley W G , Hollowood D L , Honscheid K , James D J , Kuropatkin N , Li T S , Lima M , Lin H , Maia M A G , Marshall J L , Melchior P , Menanteau F , Miquel R , Palmese A , Paz-Chinchón F , Plazas A A , Roodman A , Rykoff E S , Sanchez E , Santiago B , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Suchyta E , Swanson M E C , Tarle G , Tucker D L , Varga T N , Walker A R , Wester W , Wilkinson R D ,   (DES Collaboration)
Published: May 2020

We present a description of the Australian Dark Energy Survey (OzDES) and summarize the results from its 6 years of operations. Using the 2dF fibre positioner and AAOmega spectrograph on the 3.9-m Anglo-Australian Telescope, OzDES has monitored 771 active galactic nuclei, classified hundreds of supernovae, and obtained redshifts for thousands of galaxies that hosted a transient within the 10 deep fields of the Dark Energy Survey. We also present the second OzDES data release, containing the redshifts of almost 30 000 sources, some as faint as rAB = 24 mag, and 375 000 individual spectra. These data, in combination with the time-series photometry from the Dark Energy Survey, will be used to measure the expansion history of the Universe out to z ∼ 1.2 and the masses of hundreds of black holes out to z ∼ 4. OzDES is a template for future surveys that combine simultaneous monitoring of targets with wide-field imaging cameras and wide-field multi-object spectrographs.
The predicted properties of helium-enriched globular cluster progenitors at high redshift
Authors: Nataf David M , Horiuchi Shunsaku , Costa Guglielmo , Wyse Rosemary F G , Ting Yuan-Sen , Crocker Roland , Federrath Christoph , Chen Yang
Published: May 2020

Globular cluster progenitors may have been detected by Hubble Space Telescope, and are predicted to be observable with James Webb Space Telescope (JWST) and ground-based extremely large telescopes with adaptive optics. This has the potential to elucidate the issue of globular cluster formation and the origins of significantly helium-enriched subpopulations, a problem in Galactic astronomy with no satisfactory theoretical solution. Given this context, we use model stellar tracks and isochrones to investigate the predicted observational properties of helium-enriched stellar populations in globular cluster progenitors. We find that, relative to helium-normal populations, helium-enriched (ΔY = +0.12) stellar populations similar to those inferred in the most massive globular clusters, are expected, modulo some rapid fluctuations in the first ∼30 Myr, to be brighter and redder in the rest frame. At fixed age, stellar mass, and metallicity, a helium-enriched population is predicted to converge to being ∼0.40 mag brighter at $\lambda \approx 2.0\, {\mu \rm m}$, and to be 0.30-mag redder in the JWST–NIRCam colour (F070W − F200W), and to actually be fainter for $\lambda \lesssim 0.50 \, {\mu \rm m}$. Separately, we find that the time-integrated shift in ionizing radiation is a negligible $\sim \!5{{\ \rm per\ cent}}$, though we show that the Lyman-α escape fraction could end up higher for helium-enriched stars.
Classification of 6D Leibniz algebras
Authors: Hlavatý Ladislav
Published: May 2020

Leibniz algebras ${\mathcal E}_n$ were introduced as an algebraic structure underlying U-duality. Algebras ${\mathcal E}_3$ derived from Bianchi 3D Lie algebras are classified here. Two types of algebras are obtained: 6D Lie algebras that can be considered an extension of the semi-Abelian 4D Drinfel’d double and unique extensions of non-Abelian Bianchi algebras. For all of the algebras explicit forms of generalized frame fields are given.
HyPE study: hydroxychloroquine prophylaxis-related adverse events’ analysis among healthcare workers during COVID-19 pandemic: a rising public health concern
Authors: Nagaraja Bada Sharanappa , Ramesh Kalhalli Narayanaswamy , Dhar Debjyoti , Mondal Mahammad Samim , Dey Treshita , Saha Subhrakamal , Khan Mumtaz Ali , Rutul Shah Dhiren , Pratik Kishore , Manjula Jayaram , Sangeeth Thuppanattumadam Ananthasubramanian , Singh Vikram
Published: May 2020

Background

The rising burden of Coronavirus disease (COVID-19) has led to the mass use of hydroxychloroquine by healthcare workers (HCWs). Adverse event profile of this drug when used as prophylaxis is not well known in the literature.

Methods

A retrospective, cross-sectional study was conducted across the country using semi-structured web-based questionnaire among COVID-19 negative and asymptomatic healthcare workers, taking hydroxychloroquine prophylaxis. Descriptive and multivariate logistic-regression models were applied for analysis.

Results

Of the 166 participants, at least one adverse event was experienced by 37.9% participants, gastrointestinal being the most common (30.7%). Risk was higher in participants <40 years age (odd’s ratio (OR): 2.44, 95% confidence interval (CI): 1.18–5.05) and after first dose of hydroxychloroquine (51.2%, OR: 2.38, 95%CI: 1.17–4.84). Hydroxychloroquine prophylaxis was initiated without electrocardiography by 80.1% of HCWs. Only 21.6% of those with cardiovascular disease could get prior ECG.

Conclusions

A higher incidence of adverse events was observed when results were compared with studies involving patients on long-term hydroxychloroquine therapy. Younger age and first dose were associated with greater incidence of adverse events though all were self-limiting. Monitoring prior and during prophylaxis was inadequate even among those with cardiovascular disease and risk-factors. However, no serious cardiovascular events were reported.
Quantification of the Uncertainties in Extrapolating From In Vitro Androgen Receptor Antagonism to In Vivo Hershberger Assay Endpoints and Adverse Reproductive Development in Male Rats
Authors: Gray Leon E , Furr Johnathan R , Lambright Christy S , Evans Nicola , Hartig Phillip C , Cardon Mary C , Wilson Vickie S , Hotchkiss Andrew K , Conley Justin M
Published: May 2020

Multiple molecular initiating events exist that disrupt male sexual differentiation in utero including androgen receptor (AR) antagonism and inhibition of synthesis, and metabolism of fetal testosterone. Disruption of androgen signaling by AR antagonists in utero reduces anogenital distance (AGD) and induces malformations in F1 male rat offspring. We are developing a quantitative network of adverse outcome pathways that includes multiple molecular initiating events and key events linking anti-AR activities to permanent reproductive abnormalities. Here, our objective was to determine how accurately the EC50s for AR antagonism in vitro or ED50s for reduced tissue growth in the Hershberger assay (HA) (key events in the adverse outcome pathway) predict the ED50s for reduced AGD in male rats exposed in utero to AR antagonists. This effort included in-house data and published studies from the last 60 years on AR antagonism in vitro and in vivo effects in the HA and on AGD after in utero exposure. In total, more than 250 studies were selected and included in the analysis with data from about 60 potentially antiandrogenic chemicals. The ability to predict ED50s for key events and adverse developmental effects from the in vitro EC50s displays considerable uncertainty with R2 values for HA and AGD of < 6%. In contrast, there is considerably less uncertainty in extrapolating from the ED50s in the HA to the ED50s for AGD (R2 value of about 85%). In summary, the current results suggest that the key events measured in the HA can be extrapolated with reasonable certainty to predict the ED50s for the adverse in utero effects of antiandrogenic chemicals on male rat offspring.
Physiologically Based Pharmacokinetic Modeling in Risk Assessment: Case Study With Pyrethroids
Authors: Mallick Pankajini , Song Gina , Efremenko Alina Y , Pendse Salil N , Creek Moire R , Osimitz Thomas G , Hines Ronald N , Hinderliter Paul , Clewell Harvey J , Lake Brian G , Yoon Miyoung , Moreau Marjory
Published: May 2020

The assessment of potentially sensitive populations is an important application of risk assessment. To address the concern for age-related sensitivity to pyrethroid insecticides, life-stage physiologically based pharmacokinetic (PBPK) modeling supported by in vitro to in vivo extrapolation was conducted to predict age-dependent changes in target tissue exposure to 8 pyrethroids. The purpose of this age-dependent dosimetry was to calculate a Data-derived Extrapolation Factor (DDEF) to address age-related pharmacokinetic differences for pyrethroids in humans. We developed a generic human PBPK model for pyrethroids based on our previously published rat model that was developed with in vivo rat data. The results demonstrated that the age-related differences in internal exposure to pyrethroids in the brain are largely determined by the differences in metabolic capacity and in physiology for pyrethroids between children and adults. The most important conclusion from our research is that, given an identical external exposure, the internal (target tissue) concentration is equal or lower in children than in adults in response to the same level of exposure to a pyrethroid. Our results show that, based on the use of the life-stage PBPK models with 8 pyrethroids, DDEF values are essentially close to 1, resulting in a DDEF for age-related pharmacokinetic differences of 1. For risk assessment purposes, this indicates that no additional adjustment factor is necessary to account for age-related pharmacokinetic differences for these pyrethroids.
Characterizations of Human UDP-Glucuronosyltransferase Enzymes in the Conjugation of p-Cresol
Authors: Rong Yan , Kiang Tony K L
Published: May 2020

p-Cresol is a uremic toxin that is formed by intestinal microbiota and extensively conjugated by first-pass metabolism. p-Cresol glucuronide exerts various forms of cellular toxicity in vitro and is accumulated in the plasma of subjects with kidney disease, where associations with adverse cardiovascular and renal outcomes are evident. The objective of this study was to determine the contributions of human UDP-glucuronosyltransferase (UGT) enzymes in the formation of p-cresol glucuronide. Utilizing commonly expressed hepatic or renal human recombinant UGTs (ie, hrUGT1A1, 1A3, 1A4, 1A6, 1A7, 1A8, 1A9, 1A10, 2B4, 2B7, 2B10, 2B15, and 2B17), hrUGT1A6 and hrUGT1A9 exhibited the highest catalytic activities in the generation of p-cresol glucuronide. The kinetics of p-cresol glucuronide formation in hrUGT1A6 and pooled human liver microsomes were best described by the Hill equation and in hrUGT1A9 and pooled human kidney microsomes by substrate inhibition. Using inhibitory and selective UGT inhibitors (ie, acetaminophen or amentoflavone for UGT1A6 and niflumic acid for UGT1A9), UGT1A6 was identified the predominant enzyme responsible for p-cresol glucuronide production in pooled human liver (78.4%–81.3% contribution) and kidney (54.3%–62.9%) microsomes, whereas UGT1A9 provided minor contributions (2.8% and 35.5%, respectively). The relative contributions of UGT1A6 (72.6 ± 11.3%, mean ± SD) and UGT1A9 (5.7 ± 4.1%) in individual human liver microsomes from 12 adult donors were highly variable, where an inverse association (R = −.784, p = .003) between UGT1A6 contribution and UGT1A9 probe substrate activity (ie, mycophenolic acid) was evident. Our novel findings provide valuable tools for conducting further mechanistic studies and for designing clinical interventions to mitigate the toxicities associated with p-cresol glucuronide.
RETRACTED: Long non-coding RNA LINC00346 contributes to cisplatin resistance in nasopharyngeal carcinoma by repressing miR-342-5p
Authors: Cui Zheqing , Pu Tian , Zhang Yujie , Wang Jia , Zhao Yulin
Published: May 2020

Cisplatin has been used as the first-line chemotherapy to treat advanced nasopharyngeal carcinoma (NPC), while acquired cisplatin resistance resulting from epigenetic regulation is not well understood. The relative expression of LINC00346 was detected in healthy persons, cisplatin-sensitive (CS) patients and cisplatin-resistant (CR) patients. The regulatory effect of LINC00346 on the proliferation was detected by cell-counting kit-8. Apoptosis was assayed by histone/DNA ELISA and Caspase-3 activity. Clonal formation and cisplatin resistance were also deciphered. Luciferase reporter and RNA immunoprecipitation assay were adopted to study the interaction between LINC00346 and miR-342-5p. LINC00346 was highly expressed in NPC patients, especially in CR patients, which was associated with cisplatin resistance and poor prognosis. Inhibition of LINC00346 expression promoted cisplatin sensitivity of NPC cells, while LINC00346 over-expression promoted cisplatin resistance of NPC cells. miR-342-5p expression was negatively correlated with cisplatin resistance, and microRNA-342-5p siRNAs treatment could rescue the cisplatin resistance diminished by LINC00346 inhibition. It was further found that miR-342-5p was negatively regulated by LINC00346. In conclusion, LINC00346 regulates the cisplatin resistance of NPC cells by inhibiting miR-342-5p, which could provide a potential target for chemotherapy resistance.
Cooperation with closely bonded individuals reduces cortisol levels in long-tailed macaques
Authors: Stocker Martina , Loretto Matthias-Claudio , Sterck Elisabeth H. M. , Bugnyar Thomas , Massen Jorg J. M.
Published: May 2020

Many animal species cooperate with conspecifics in various social contexts. While ultimate causes of cooperation are being studied extensively, its proximate causes, particularly endocrine mechanisms, have received comparatively little attention. Here, we present a study investigating the link between the hormone cortisol, cooperation and social bonds in long-tailed macaques (
Macaca fascicularis
). We tested 14 macaques in a dyadic cooperation task (loose-string paradigm), each with two partners of different social bond strength and measured their salivary cortisol before and after the task. We found no strong link between the macaques' cortisol level before the task and subsequent cooperative success. By contrast, we did find that the act of cooperating in itself led to a subsequent decrease in cortisol levels, but only when cooperating with closely bonded individuals. Two control conditions showed that this effect was not due to the mere presence of such an individual or the pulling task itself. Consequently, our study shows an intricate way in which the hypothalamic–pituitary–adrenal axis is involved in cooperation. Future studies should reveal whether and how our findings are driven by the anxiolytic effect of oxytocin, which has been associated with social bonding.
Predicting human complexity perception of real-world scenes
Authors: Nagle Fintan , Lavie Nilli
Published: May 2020

Perceptual load is a well-established determinant of attentional engagement in a task. So far, perceptual load has typically been manipulated by increasing either the number of task-relevant items or the perceptual processing demand (e.g. conjunction versus feature tasks). The tasks used often involved rather simple visual displays (e.g. letters or single objects). How can perceptual load be operationalized for richer, real-world images? A promising proxy is the visual complexity of an image. However, current predictive models for visual complexity have limited applicability to diverse real-world images. Here we modelled visual complexity using a deep convolutional neural network (CNN) trained to learn perceived ratings of visual complexity. We presented 53 observers with 4000 images from the PASCAL VOC dataset, obtaining 75 020 2-alternative forced choice paired comparisons across observers. Image visual complexity scores were obtained using the TrueSkill algorithm. A CNN with weights pre-trained on an object recognition task predicted complexity ratings withr= 0.83. By contrast, feature-based models used in the literature, working on image statistics such as entropy, edge density and JPEG compression ratio, only achievedr= 0.70. Thus, our model offers a promising method to quantify the perceptual load of real-world scenes through visual complexity.
Electrochemical and thermodynamic properties of 1-phenyl-3-(phenylamino)propan-1-one with Na
2
WO
4
on N80 steel
Authors: Wang Yun , Hu Jun , Zhang Lei , Cao Jiangli , Lu Minxu
Published: May 2020

The corrosion inhibition effect and adsorption behaviour of 1-phenyl-3-(phenylamino)propan-1-one (PPAPO) on N80 steel in hydrochloric acid solution have been investigated by Fourier transform infrared (FTIR), electrochemical method and scanning electron microscopy. The corrosion inhibition mechanism of PPAPO mixed with Na
2
WO
4
was interpreted from the thermodynamic point of view. The results indicated that PPAPO mixed with Na
2
WO
4
acted as a mixed-type inhibitor. The inhibition film formed on N80 steel surface can increase the charge transfer resistance and prevent the occurrence of corrosion reaction, thereby reducing the corrosion rate of metal surface. The inhibition efficiency was up to 96.65%; the inhibitor PPAPO with Na
2
WO
4
showed good synergistic effect on N80 corrosion behaviour in HCl solution. The adsorption behaviour of inhibitors on N80 steel surface was in accordance with the Langmuir adsorption model and mainly belonged to chemisorption. The adsorption process of PPAPO on N80 surface was spontaneous and irreversible endothermic reaction.
Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology
Authors: Jeantet Lorène , Planas-Bielsa Víctor , Benhamou Simon , Geiger Sebastien , Martin Jordan , Siegwalt Flora , Lelong Pierre , Gresser Julie , Etienne Denis , Hiélard Gaëlle , Arque Alexandre , Regis Sidney , Lecerf Nicolas , Frouin Cédric , Benhalilou Abdelwahab , Murgale Céline , Maillet Thomas , Andreani Lucas , Campistron Guilhem , Delvaux Hélène , Guyon Christelle , Richard Sandrine , Lefebvre Fabien , Aubert Nathalie , Habold Caroline , le Maho Yvon , Chevallier Damien
Published: May 2020

The identification of sea turtle behaviours is a prerequisite to predicting the activities and time-budget of these animals in their natural habitat over the long term. However, this is hampered by a lack of reliable methods that enable the detection and monitoring of certain key behaviours such as feeding. This study proposes a combined approach that automatically identifies the different behaviours of free-ranging sea turtles through the use of animal-borne multi-sensor recorders (accelerometer, gyroscope and time-depth recorder), validated by animal-borne video-recorder data. We show here that the combination of supervised learning algorithms and multi-signal analysis tools can provide accurate inferences of the behaviours expressed, including feeding and scratching behaviours that are of crucial ecological interest for sea turtles. Our procedure uses multi-sensor miniaturized loggers that can be deployed on free-ranging animals with minimal disturbance. It provides an easily adaptable and replicable approach for the long-term automatic identification of the different activities and determination of time-budgets in sea turtles. This approach should also be applicable to a broad range of other species and could significantly contribute to the conservation of endangered species by providing detailed knowledge of key animal activities such as feeding, travelling and resting.
Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcome
Authors: Ramlall Vijendra , Thangaraj Phyllis M. , Meydan Cem , Foox Jonathan , Butler Daniel , May Ben , De Freitas Jessica K. , Glicksberg Benjamin S. , Mason Christopher E. , Tatonetti Nicholas P. , Shapira Sagi D.
Published: May 2020

Summary

Understanding the pathophysiology of SARS-CoV-2 infection is critical for therapeutics and public health intervention strategies. Viral-host interactions can guide discovery of regulators of disease outcomes, and protein structure function analysis points to several immune pathways, including complement and coagulation, as targets of the coronavirus proteome. To determine if conditions associated with dysregulation of the complement or coagulation systems impact adverse clinical outcomes, we performed a retrospective observational study of 11,116 patients who presented with suspected SARS-CoV-2 infection. We found that history of macular degeneration (a proxy for complement activation disorders) and history of coagulation disorders (thrombocytopenia, thrombosis, and hemorrhage) are risk factors for morbidity and mortality in SARS-CoV-2 infected patients - effects that could not be explained by age, sex, or history of smoking. Further, transcriptional profiling of nasopharyngeal (NP) swabs from 650 control and SARS-CoV-2 infected patients demonstrated that in addition to innate Type-I interferon and IL-6 dependent inflammatory immune responses, infection results in robust engagement and activation of the complement and coagulation pathways. Finally, we conducted a candidate driven genetic association study of severe SARS-CoV-2 disease. Among the findings, our scan identified putative complement and coagulation associated loci including missense, eQTL and sQTL variants of critical regulators of the complement and coagulation cascades. In addition to providing evidence that complement function modulates SARS-CoV-2 infection outcome, the data point to putative transcriptional genetic markers of susceptibility. The results highlight the value of using a multi-modal analytical approach, combining molecular information from virus protein structure-function analysis with clinical informatics, transcriptomics, and genomics to reveal determinants and predictors of immunity, susceptibility, and clinical outcome associated with infection.
Placental pathology in COVID-19
Authors: Shanes Elisheva D , Mithal Leena B , Otero Sebastian , Azad Hooman A , Miller Emily S , Goldstein Jeffery A
Published: May 2020

Objectives: To describe histopathologic findings in the placentas of women with COVID-19 during pregnancy.

Methods: Pregnant women with COVID-19 delivering between March 18, 2020 and May 5, 2020 were identified. Placentas were examined and compared to historical controls and women with placental evaluation for a history of melanoma.

Results: 16 placentas from patients with SARS-CoV-2 were examined (15 with live birth in the 3rd trimester 1 delivered in the 2nd trimester after intrauterine fetal demise). Compared to controls, third trimester placentas were significantly more likely to show at least one feature of maternal vascular malperfusion (MVM), including abnormal or injured maternal vessels, as well as delayed villous maturation, chorangiosis, and intervillous thrombi. Rates of acute and chronic inflammation were not increased.
The placenta from the patient with intrauterine fetal demise showed villous edema and a retroplacental hematoma.

Conclusions: Relative to controls, COVID-19 placentas show increased prevalence of features of maternal vascular malperfusion (MVM), a pattern of placental injury reflecting abnormalities in oxygenation within the intervillous space associated with adverse perinatal outcomes. Only 1 COVID-19 patient was hypertensive despite the association of MVM with hypertensive disorders and preeclampsia. These changes may reflect a systemic inflammatory or hypercoagulable state influencing placental physiology.
The timing of contact restrictions and pro-active testing balances the socio-economic impact of a lockdown with the control of infections
Authors: Bej Saptarshi , Wolkenhauer Olaf
Published: May 2020

During the SARS-CoV-2 pandemic, numerous mathematical models have been developed. Reporting artefacts and missing data about asymptomatic spreaders, imply considerable margins of uncertainty for model-based predictions. Epidemiological models can however also be used to investigate the consequences of measures to control the pandemic, reflected in changes to parameter values.

We present a SIR-based, SUIR model in which the influence of testing and a reduction of contacts is studied by distinguishing ‘Unidentified’ and ‘Identified’ spreaders of infections. The model uses four ordinary differential equations and is kept deliberately simple to investigate general patterns occurring from testing and contact restrictions. The model goes beyond other efforts, by introducing time dependent parameter curves that represent different strategies in controlling the pandemic.

Our analysis reveals the effect of ‘pro-active’ testing for the design of contact restriction measures. By pro-active testing we mean testing beyond those people who show symptoms. The simulations can explain why the timing of contract restrictions and pro-active testing is important. The model can also be used to study the consequence of different strategies to exit from lockdown.

Our SUIR model is implemented in Python and is made available through a Juypter Notebooks. This an extensive documentation of the derivation and implementation of the model, as well as transparent and reproducible simulation studies. Our model should contribute to a better understanding of the role of testing and contact restrictions.
Evolving Epidemiology and Effect of Non-pharmaceutical Interventions on the Epidemic of Coronavirus Disease 2019 in Shenzhen, China
Authors: Huang Suli , Zhang Zhen , Wu Yongsheng , Mei Shujiang , Li Yuan , Xie Xu , Liu Xiaojian , Tang Xiujuan , Kong Dongfeng , Wu Xiaoliang , Wu Yu , Wei Lan , Lv Ziquan , Yu Shuyuan , Wen Ying , Zhou Guohong , Chen Tianmu , Feng Tiejian , Zou Xuan
Published: May 2020

Previous studies have demonstrated the characteristics of patients with 2019 novel coronavirus disease (COVID-19). However, the effect of non-pharmaceutical interventions on the epidemic in Shenzhen, China remains unknown. Individual data of 417 cases were extracted from the epidemiological investigations and the National Infectious Disease Information System between January 1, 2020 and February 29, 2020. On the basis of important interventions, the epidemic was divided into four periods (January 1-15, January 16-22, January 23-February 5 and after February 6). We used a susceptible-exposed-infectious-asymptomatic-recovered model to evaluate the effect of interventions. Results suggested that about 53.7% were imported from Wuhan. The median age was 47 years and 52.8% were women. Severity risk increased with age and associated with male and co-existing disorders. The attack rate peaked in the third period and drastically decreased afterwards across sex, age groups and geographic regions. Children younger than 5 years showed a higher attack rate than those aged of 6~19. The effective reproductive number decreased from 1.44 to 0.05 after the highest level emergency response since January 23. Overall, the non-pharmaceutical interventions have effectively mitigated the COVID-19 outbreak in Shenzhen, China. These findings may facilitate the introduction of public health policies in other countries and regions.
Early Awake Prone and Lateral Position in Non-intubated Severe and Critical Patients with COVID-19 in Wuhan: A Respective Cohort Study
Authors: Dong Wei , Gong Yiping , Feng Juan , Bai Lang , Qing Haomiao , Zhou Peng , Du Yu , Zhu Junchen , Xu Shanling
Published: May 2020

Background
Previous studies suggest applying prone position (PP) and lateral position (LP) in patients with severe acute respiratory distress syndrome (ARDS) for their efficacy in improving oxygenation and lung recruitment.This paper aims to share clinical experiences and outcome of using PP and LP in combination with oxygen therapy (OT) and Non-invasive ventilation (NIV) in severe and critical patients with COVID-19.

Methods
Clinical data of 48 severe and critical patients have been retrieved from medical records and reviewed. The primary outcome is the survival rate. Secondary outcome is the rate of patients requiring intubation.

Results
In total, 25 patients were finally included in the study.The mean respiratory rate of all 25 patients decreased from 28.4 breaths/min to 21.3 breaths/min. CT results showed increase in lung recruitment. All patients tolerated PP and LP well. No deterioration or severe adverse events associated with PP and LP occurred. All patients recovered and survived without intubation. Follow-up to date showed that all patients have been discharged except one with mild symptoms and positive RNA test.

Conclusion:
Clinical outcomes of early application of PP and LP in combination with OT and NIV in severe and critical patients with COVID-19 indicated well tolerance of the therapy and resulted in improving patients' oxygenation in a safe and effective manner. Therefore, this strategy can be explored as an early intervention in managing patients in early stage of disease development under the context of pandemic and limited medical resources.
Breaking the back of COVID-19: Is Bangladesh doing enough testing?
Authors: Rahaman Khan Hasinur , Howlader Tamanna
Published: May 2020

Following detection of the first 100 confirmed cases of COVID-19 in early April, Bangladesh stepped up its efforts to strengthen testing capacity in order to curb the spread of the disease across the country. This paper sheds light on the position of Bangladesh in relation to its South Asian neighbors India and Pakistan with respect to testing capacity and ability to detect cases with increased testing. It also analyzes recent data on case counts and testing numbers in Bangladesh, to provide an idea regarding the number of extra tests needed to detect a substantial number of cases within a short period of time. Findings indicate that compared to India and Pakistan, Bangladesh was able to detect more cases by increasing testing levels and expand its testing capacity by performing more per capita tests. In spite of these achievements, the rate of reported cases per 100 tests was consistently higher for Bangladesh compared to India, which suggests that in addition to increased testing, other factors, such as, effective enforcement of social distancing and efficient contact tracing are just as important in curbing the spread of the disease. The analysis reveals that current testing levels in Bangladesh are not adequate. Based on the findings, we recommend a 30-50\% growth of the current test rate in the next few days so that by detecting and isolating more cases, Bangladesh could, in effect, contain the spread of new infections. The challenge, however, is to mobilize resources necessary to expand geographical coverage and improve testing quality while enforcing social distancing and performing efficient contact tracing.
Effect of preventive actions and health care factors in controlling the outbreaks of COVID-19 pandemic
Authors: Abdulla Faruq , Nain Zulkar , Karimuzzaman Md. , Hossain Md. Moyazzem , Adhikari Utpal Kumar , Rahman Azizur
Published: May 2020

With the insurgence of the COVID-19 pandemic, a large number of people died in the past several months, and the situation is ongoing with increasing health, social and economic panic and vulnerability. Due to the lack of drugs and prophylaxis against COVID-19, most of the countries are now relying on maintaining social distance as preventative actions. However, this social distancing can create global socio-economic crisis and psychological disorders. Therefore, these control measures need to have an assessment to evaluate their value in containing the situation. In this study, we analyzed the outcome of COVID-19 in response to different control measures, health care facilities, and prevalent diseases. Based on our findings, the number of COVID-19 deaths found to be reduced with increased medical personnel and hospital beds. We found 0.23, 0.16, and 0.21 as the measurement of significant non-linear relationship between COVID-19 case fatality and number of physicians (p-value ≤ 7.1×10−6), nurses and midwives (p-value ≤ 4.6×10−3), and hospital beds (p-value ≤ 1.9×10−2). Importantly, we observed a significant correlation between the reduction of COVID-19 cases and the earliness of preventive initiation. As a result, enhancing health care facilities as well as imposing the control measures in a short time could be valuable to prevent the currently raging COVID-19 pandemic. The apathy of taking nation-wide immediate precaution measure has identified as one of the critical reasons to make the circumstances worst. Notably, countries including Gambia, Nicaragua, Burundi, Namibia, and Nepal have marked in a state of danger. Interestingly, no association between the comorbidities and severity of COVID-19 was found except for few diseases including cancer, which warranted further investigation at the pathobiological level. We believe that this study could be useful in developing a control strategy in COVID-19 as well as future pandemics.
Higher Temperature, Pressure, and Ultraviolet Are Associated with Less COVID-19 Prevalence – Meta-Regression of Japanese Prefectural Data
Authors: Takagi Hisato , Kuno Toshiki , Yokoyama Yujiro , Ueyama Hiroki , Matsushiro Takuya , Hari Yosuke , Ando Tomo
Published: May 2020

A recent study from China suggests that high temperature and ultraviolet (UV) radiation cannot decrease the epidemics of Coronavirus disease 2019 (COVID-19). To determine whether COVID-19 prevalence is modulated by meteorological conditions, meta-regression of Japanese prefectural data was herein conducted. We extracted integrated number of patients testing positive for COVID-19 in each Japanese prefecture on 18 May 2020, population per 1-km2 inhabitable area in the prefecture in 2020, and monthly meteorological conditions at each prefectural capital city for 4 months (from January to April 2020). We averaged or cumulated the monthly data for the 4 months. To adjust for prefectural population density, we defined the COVID-19 prevalence as the integrated number of patients testing positive divided by the population per 100-km2 inhabitable area. Random-effects meta-regression was performed. A slope of the meta-regression line was significantly negative for mean air temperature (coefficient, −0.134; P = 0.019), mean sea level air pressure (−0.351; P = 0.001), and mean daily maximum UV index (−0.908; P = 0.012), which indicated that COVID-19 prevalence decreased significantly as air temperature, air pressure, and UV index increased. In conclusion, higher temperature, pressure, and UV may be associated with less COVID-19 prevalence, which should be confirmed by further epidemiological investigations taking other risk and protective factors of COVID-19 into account.
Local computational methods to improve the interpretability and analysis of cryo-EM maps
Authors: Kaur S. , Gomez-Blanco J. , Khalifa A. , Adinarayanan S. , Sanchez-Garcia R. , Wrapp D. , McLellan J. S. , Bui K. H. , Vargas J.
Published: May 2020

Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, ‘over-sharpening’ due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e.ab initiomodelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.
DNA ligases ofProchlorococcus marinus: an evolutionary exception to the rules of replication
Authors: Hjerde Erik , Maguren Ashleigh , Rzoska-Smith Elizabeth , Kirby Bronwyn , Williamson Adele
Published: May 2020

DNA ligases, essential enzymes which re-join the backbone of DNA come in two structurally-distinct isoforms, NAD-dependent and ATP-dependent, which differ in cofactor usage. The present view is that all bacteria exclusively use NAD-dependent DNA ligases for DNA replication, while archaea and eukaryotes use ATP-dependent DNA ligases. Some bacteria also possess auxiliary ATP-dependent DNA ligases; however, these are only employed for specialist DNA repair processes. Here we show that in the genomes of high-light strains of the marine cyanobacteriumProchlorococcocus marinus, an ATP-dependent DNA ligase has replaced the NAD-dependent form, overturning the present paradigm of a clear evolutionary split in ligase usage. Genes encoding partial NAD-dependent DNA ligases are found on mobile regions in highlight genomes and lack domains required for catalytic function. This constitutes the first reported example of a bacterium that relies on an ATP-dependent DNA ligase for DNA replication and recommendsP. marinusas a model to investigate the evolutionary origins of these essential DNA-processing enzymes.
Hematopoietic progenitors polarize in contact with bone marrow stromal cells by engaging CXCR4 receptors
Authors: Bessy Thomas , Souquet Benoit , Vianay Benoit , Schaeffer Alexandre , Jaffredo Thierry , Larghero Jerome , Blanchoin Laurent , Brunet Stephane , Faivre Lionel , Théry Manuel
Published: May 2020

Hematopoietic stem and progenitor cells (HSPCs) are located in the bone marrow, where they regulate the permanent production and renewal of all blood-cell types. HSPC proliferation and differentiation is locally regulated by their interaction with cells forming specific microenvironments close to the bone matrix or close to blood vessels. However, the cellular mechanisms underlying HSPC’s interaction with these cells and their potential impact on HSPC polarity is still poorly understood. Here we modelled the bone-marrow niche using microfluidic technologies in a bone-marrow on a chip device, and evaluated long-duration cell-cell contacts between single HSPCs and stromal cells or endothelial cells in a custom-designed microwell cell-culture system. We found that an HSPC can form a discrete contact site that leads to the extensive polarization of their cytoskeleton architectures. As in the case with immune synapses formed by lymphocytes, the centrosome was located in proximity of the cell-cell contact. The entire microtubule network emanated from the centrosome, and the nucleus was confined to the side opposite of the cell-cell contact. The capacity of the HSPC to polarize appeared specific as it was not observed in contact with skin fibroblasts. The receptors ICAM, VCAM and CXCR4 were identified in the polarizing contact, and were all independently capable of inducing morphological polarization. However, only CXCR4 was independently capable of inducing the polarization of the centrosome-microtubule network. Altogether these results revealed a novel mechanism of HSPC polarization associated with its anchorage to specific cells in the bone-marrow, which might be instrumental in the regulation of their fate.
ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens
Authors: Zamecnik Colin R. , Rajan Jayant V. , Yamauchi Kevin A. , Mann Sabrina A. , Sowa Gavin M. , Zorn Kelsey C. , Alvarenga Bonny D. , Stone Mars , Norris Philip J. , Gu Wei , Chiu Charles Y , DeRisi Joseph L. , Wilson Michael R
Published: May 2020

Serologic assays are needed to determine SARS-CoV-2 seroprevalence, but poor specificity can overestimate exposures. Here, we built a pan-human coronavirus proteome-wide programmable phage display assay (VirScan) to profile coronavirus antigens specifically enriched by 20 COVID-19 patient serum IgG. With ReScan, a new diagnostic development workflow which combines the isolation of phage expressing the most immunogenic peptides with paper-based microarrays manufactured via acoustic liquid handling, we identified 9 candidate antigens from a library of 534 SARS-CoV-2 peptides. These arrays could form the basis of a multiplexed COVID-19 serologic assay with enhanced specificity. ReScan has broad applicability for serologic assay development.
Root specific plasticity induced by paclobutrazol confers improved deficit irrigation tolerance and agronomic performance in maize
Authors: Urfan Mohammad , Hakla Haroon Rashid , Sharma Shubham , Khajuria Manu , Satbhai Santosh B. , Vyas Dhiraj , Bhougal Sunil , Yadav Narendra Singh , Pal Sikander
Published: May 2020

Drought stress in maize often results in poor growth and reduced yield. Antioxidants play vital role in management of abiotic stresses. Drought or water deficit are detrimental to young seedlings establishment and transition from vegetative to reproductive growth in maize. Paclobutrazol (PBZ) has been widely used to confer abiotic stress tolerance in plants, however, its impact on root developmental attributes in maize and their relevance in drought management are least understood. Comprehensive experiments over a three year period (2017-2019) under early deficit (EDI) and terminal deficit (TDI) irrigation with or without paclobutrazol (PBZ) were conducted on five maize varieties (DDKL, DKC-9144, PG-2475, PG-2320 and Bio-9621). Plant shoot and root growth kinetics, phenological changes and physiological perturbations including antioxidant profile coupled with molecular regulation of root traits, showed DKC-9144 as best variety in terms of plant fitness and reproductive performance under deficit irrigation. Root developmental rates were key contributors towards improved plant biomass and cob yield under deficit irrigation tolerance. Structural equation modelling (SEM) demonstrated specific contribution of different root types (crown, brace and seminal roots) in maize towards improving water use efficiency, cob yield and plant height. From SEM, seminal root surface area and root length are proposed desired traits to improve water use efficiency and cob yield in DKC-9144 under deficit irrigation. Bi-variate analyses of twenty key traits of plant fitness and agronomic importance showed a strong correlation (r) between root traits and improved growth performance and yield stability indices.