bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiomics-based characterization of specialized metabolites biosynthesis in Cornus Officinalis
Authors: Rai Amit , Rai Megha , Kamochi Hidetaka , Mori Tetsuya , Nakabayashi Ryo , Nakamura Michimi , Suzuki Hideyuki , Saito Kazuki , Yamazaki Mami
Published: May 2020

Cornus officinalis, an important traditional medicinal plant, is used as major constituents of tonics, analgesics, and diuretics. While several studies have focused on its characteristic bioactive compounds, little is known on their biosynthesis. In this study, we performed LC-QTOF-MS-based metabolome and RNA-seq-based transcriptome profiling for seven tissues of C. officinalis. Untargeted metabolome analysis assigned chemical identities to 1,215 metabolites and showed tissue-specific accumulation for specialized metabolites with medicinal properties. De novo transcriptome assembly established for C. officinalis showed 96% of transcriptome completeness. Co-expression analysis identified candidate genes involved in the biosynthesis of iridoids, triterpenoids, and gallotannins, the major group of bioactive metabolites identified in C. officinalis. Integrative omics analysis identified 45 cytochrome P450s genes correlated with iridoids accumulation in C. officinalis. Network-based integration of genes assigned to iridoids biosynthesis pathways with these candidate CYPs further identified seven promising CYPs associated with iridoids’ metabolism. This study provides a valuable resource for further investigation of specialized metabolites’ biosynthesis in C. officinalis.
Micromagnetic simulations of first-order reversal curve (FORC) diagrams of framboidal greigite
Authors: Valdez-Grijalva Miguel A , Nagy Lesleis , Muxworthy Adrian R , Williams Wyn , Roberts Andrew P , Heslop David
Published: May 2020

Greigite is a sensitive environmental indicator and occurs commonly in nature as magnetostatically interacting framboids. Until now only the magnetic response of isolated non-interacting greigite particles have been modelled micromagnetically. We present here hysteresis and first-order reversal curve (FORC) simulations for framboidal greigite (Fe3S4), and compare results to those for isolated particles of a similar size. We demonstrate that these magnetostatic interactions alter significantly the framboid FORC response compared to isolated particles, which makes the magnetic response similar to that of much larger (multidomain) grains. We also demonstrate that framboidal signals plot in different regions of a FORC diagram, which facilitates differentiation between framboidal and isolated grain signals. Given that large greigite crystals are rarely observed in microscopy studies of natural samples, we suggest that identification of multidomain-like FORC signals in samples known to contain abundant greigite could be interpreted as evidence for framboidal greigite.
Time–frequency windowing in multiparameter elastic FWI of shallow seismic wavefield
Authors: Athanasopoulos Nikolaos , Manukyan Edgar , Bohlen Thomas , Maurer Hansruedi
Published: May 2020

Full-waveform inversion of shallow seismic wavefields is a promising method to infer multiparameter models of elastic material properties (S-wave velocity, P-wave velocity and mass density) of the shallow subsurface with high resolution. Previous studies used either the refracted Pwaves to reconstructed models of P-wave velocity or the high-amplitude Rayleigh waves to infer the S-wave velocity structure. In this work, we propose a combination of both wavefields using continuous time–frequency windowing. We start with the contribution of refracted P waves and gradually increase the time window to account for scattered body waves, higher mode Rayleigh waves and finally the fundamental Rayleigh wave mode. The opening of the time window is combined with opening the frequency bandwidth of input signals to avoid cycle skipping. Synthetic reconstruction tests revealed that the reconstruction of P-wave velocity model and mass density can be improved. The S-wave velocity reconstruction is still accurate and robust and is slightly benefitted by time–frequency windowing. In a field data application, we observed that time–frequency windowing improves the consistency of multiparameter models. The inferred models are in good agreement with independent geophysical information obtained from ground-penetrating radar and full-waveform inversion of SH waves.
Devolution of competition policy under the Scotland Act 2016 after Brexit: straining at the edges of the current settlement?
Authors: Andreangeli Arianna
Published: May 2020

The purpose of this article is to examine the challenges that Brexit brings for the devolution of certain aspects of competition policy to Scotland. According to section 63 of the Scotland Act 2016, Scottish Ministers can ask the Competition and Markets Authority (CMA) to carry out a phase 2 market investigation after having sought the agreement of their Westminster counterparts. This article will explore the consequences of Brexit for competition policy in the UK by placing the discussion against the broader background of the relationship existing between the central and devolved governments in the UK, with a particular emphasis on Scotland. After discussing, the nature and scope of the powers that have been devolved to the Scottish Government the article will examine the impact of Brexit on competition policy both in general and for these devolved aspects. It will be argued that the current system for the management of the inter-governmental relations between Westminster and Edinburgh may not be able to withstand the challenges brought by Brexit and affecting the role of the CMA and of the UK Government, respectively, in the fields of antitrust, state aid, and merger control.

The article will conclude that Brexit has exposed how the current framework for intergovernmental relations may not be suitable to the demands of new forms of devolution that are not predicated upon the distinction between reserved and devolved matters, but depend on the joint decision-making between the UK and the Scottish governments. Thus, unless section 63 of the Scotland Act 2016 is to remain ineffective, it may become necessary to rethink the current ways in which Scottish and UK minister interact in areas where devolution means co-decision as opposed to one government ‘giving way’ to the other.
Upscaling Pest Management From Parks to Countries: A New Zealand Case Study
Authors: Chand Ravneel R , Cridge Belinda J
Published: May 2020

Worldwide, introduced pest species create significant challenges to native biodiversity and individual health. New Zealand has an extensive history of attempting to protect biodiversity from introduced pests such as the Brushtail possum (Trichosurus vulpecula [Diprotodontia: Phalangeridae]). Success has been achieved on a small scale, but the transition to the whole country management poses new issues. Therefore, this review uses the framework of ‘Predator Free 2050’ to summarize current practices and scrutinize new technologies. Importantly, we include a toxicology focus to the discussion, providing detail on the mechanism(s) of action that inform decisions regarding the pros and cons for the use of various chemical agents. Currently, the New Zealand government supports the use of sodium fluoroacetate (1080) for predator control on a mass scale, but this comes with a social opposition that is not always reflective of the underlying science. Understanding this controversy is vital if new strategies are to be deployed to achieve large-scale pest management. We use New Zealand as a case study in this area because its unique and isolated ecosystem provides a global opportunity for understanding new technologies and best practice.
Pull-through resection without free-flap reconstruction for lateral wall oropharyngeal cancer
Authors: Matsumoto Fumihiko , Kobayashi Kenya , Omura Go , Matsumura Satoko , Matsumoto Yoshifumi , Fukasawa Masahiko , Yoshimoto Seiichi
Published: May 2020

Background

While transoral robotic surgery (TORS) is widely used for the management of lateral wall oropharyngeal carcinomas (OPC), open surgical techniques are still used in some cases. A pull-through method for open surgical resections of OPC has recently been introduced. We improved on this method by eliminating the need for subsequent free-flap reconstruction.

Methods

16 patients with lateral wall OPC underwent pull-through resections. After resection, we used the digastric muscle, stylohyoid muscles, submandibular gland and the surrounding tissues to block the neck and oral cavity and to avoid reconstruction.

Results

This novel technique was performed without major complications or morbidities. The average post-operative hospital stay was 14.6 ± 6.1 days, and the average duration until initiation of oral intake post-operation was 6.5 ± 2.9 days. Oncological outcomes, post-operative course and function were acceptable.

Conclusions

Our novel method provides an efficient and less invasive surgical technique than conventional open approaches.
Postmenopausal Hormone Therapy and Colorectal Cancer Risk by Molecularly Defined Subtypes and Tumor Location
Authors: Labadie Julia D , Harrison Tabitha A , Banbury Barbara , Amtay Efrat L , Bernd Sonja , Brenner Hermann , Buchanan Daniel D , Campbell Peter T , Cao Yin , Chan Andrew T , Chang-Claude Jenny , English Dallas , Figueiredo Jane C , Gallinger Steven J , Giles Graham G , Gunter Marc J , Hoffmeister Michael , Hsu Li , Jenkins Mark A , Lin Yi , Milne Roger L , Moreno Victor , Murphy Neil , Ogino Shuji , Phipps Amanda I , Sakoda Lori C , Slattery Martha L , Southey Melissa C , Sun Wei , Thibodeau Stephen N , Van Guelpen Bethany , Zaidi Syed H , Peters Ulrike , Newcomb Polly A
Published: May 2020

Background

Postmenopausal hormone therapy (HT) is associated with a decreased colorectal cancer (CRC) risk. As CRC is a heterogeneous disease, we evaluated whether the association of HT and CRC differs across etiologically relevant, molecularly defined tumor subtypes and tumor location.

Methods

We pooled data on tumor subtypes (microsatellite instability status, CpG island methylator phenotype status, BRAF and KRAS mutations, pathway: adenoma-carcinoma, alternate, serrated), tumor location (proximal colon, distal colon, rectum), and HT use among 8220 postmenopausal women (3898 CRC cases and 4322 controls) from 8 observational studies. We used multinomial logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CIs) for the association of ever vs never HT use with each tumor subtype compared with controls. Models were adjusted for study, age, body mass index, smoking status, and CRC family history. All statistical tests were 2-sided.

Results

Among postmenopausal women, ever HT use was associated with a 38% reduction in overall CRC risk (OR =0.62, 95% CI = 0.56 to 0.69). This association was similar according to microsatellite instability, CpG island methylator phenotype and BRAF or KRAS status. However, the association was attenuated for tumors arising through the serrated pathway (OR = 0.81, 95% CI = 0.66 to 1.01) compared with the adenoma-carcinoma pathway (OR = 0.63, 95% CI = 0.55 to 0.73; Phet =.04) and alternate pathway (OR = 0.61, 95% CI = 0.51 to 0.72). Additionally, proximal colon tumors had a weaker association (OR = 0.71, 95% CI = 0.62 to 0.80) compared with rectal (OR = 0.54, 95% CI = 0.46 to 0.63) and distal colon (OR = 0.57, 95% CI = 0.49 to 0.66; Phet =.01) tumors.

Conclusions

We observed a strong inverse association between HT use and overall CRC risk, which may predominantly reflect a benefit of HT use for tumors arising through the adenoma-carcinoma and alternate pathways as well as distal colon and rectal tumors.
Impact of a Best Practice Advisory for Pediatric Patients With Staphylococcus aureus Bacteremia
Authors: Lloyd Elizabeth C , Martin Emily T , Dillman Nicholas , Nagel Jerod , Chang Robert , Gandhi Tejal N , Tribble Alison C
Published: May 2020

Background

Infectious diseases (ID) consultation and optimal antibiotic therapy improve outcomes in Staphylococcus aureus bacteremia (SAB). Data on strategies to improve adherence to these practices in children are limited.

Methods

This was a quasi-experimental study evaluating the impact of an electronic medical record (EMR)–based best practice advisory (BPA) for SAB, recommending ID consult and optimal antibiotic therapy based on rapid mecA gene detection. Inpatients < 21 years old with SAB before (January 2015–July 2017) and after (August 2017–December 2018) BPA implementation were included. Primary outcome was receipt of ID consult. Secondary outcomes included receipt of optimal therapy, time to ID consult and optimal therapy, recurrent SAB, and 30-day all-cause mortality. ID consultation rates pre- and postimplementation were compared using interrupted time series (ITS) analysis. Hazard ratios (HRs) and 95% confidence intervals (CIs) for time to optimal therapy were calculated using Cox regression.

Results

We included 99 SAB episodes (70 preintervention, 29 postintervention). Preintervention, 48 (68.6%) patients received an ID consult compared to 27 (93.1%) postintervention, but this was not statistically significant on ITS analysis due to a preexisting trend of increasing consultation. Median hours to optimal therapy decreased from 26.1 to 5.5 (P = .03), most notably in patients with methicillin-sensitive S. aureus (MSSA) (42.2 to 10.8; P < .01). On Cox regression, BPA implementation was associated with faster time to optimal therapy (HR, 3.22 [95% CI, 1.04–10.01]).

Conclusions

Implementation of an EMR-based BPA for SAB resulted in faster time to optimal antibiotic therapy, particularly for patients with MSSA. ID consultation increased throughout the study period and was not significantly impacted by the BPA.
Sleeve gastrectomy without bougie is safe and effective operation: case report
Authors: Shekh Zkria Atia , Roqaia Abdulkafi Hasan
Published: May 2020

Sleeve gastrectomy (SG) is an effective method for weight loss; it is done by laparoscopy or open approach; it is a restrictive procedure and involves removing part of the stomach by cutting over bougie, which ensures that stenosis doesn’t occur. Bougie may cause esophageal perforation. There are studies that show the size of bougie used and weight loss are related. We show a case of open SG without using bougie at all. It is an effective and safe method and results in ~30% of weight loss 3 months after the operation without complications; thus, we conclude that SG can be done without bougie.
A case-series of bloodstream infections caused by theMeyerozyma guilliermondiispecies complex at a reference center of oncology in Brazil
Authors: Chaves Alessandra Leal Silva , Trilles Luciana , Alves Gabriela Machado , Figueiredo-Carvalho Maria Helena Galdino , Brito-Santos Fábio , Coelho Rowena Alves , Martins Ianick S , Almeida-Paes Rodrigo
Published: May 2020

Bloodstream infections (BSI) caused by Candida species are the fourth cause of healthcare associated infections worldwide. Non-albicans Candida species emerged in the last decades as agents of serious diseases. In this study, clinical and microbiological aspects of six patients with BSI due to the Meyerozyma (Candida) guilliermondii species complex from an oncology reference center in Brazil, were evaluated. To describe demographic and clinical characteristics, medical records of the patients were reviewed. Molecular identification of the isolates was performed by ITS1-5.8S-ITS2 region sequencing. Antifungal susceptibility was evaluated by the EUCAST method and the minimal inhibitory concentrations (MIC) assessed according to the epidemiological cutoff values. Virulence associated phenotypes of the isolates were also studied. Ten isolates from the six patients were evaluated. Five of them were identified as Meyerozyma guilliermondii and the others as Meyerozyma caribbica. One patient was infected with two M. caribbica isolates with different genetic backgrounds. High MICs were observed for fluconazole and echinocandins. Non-wild type isolates to voriconazole appeared in one patient previously treated with this azole. Additionally, two patients survived, despite infected with non-wild type strains for fluconazole and treated with this drug. All isolates produced hemolysin, which was not associated with a poor prognosis, and none produced phospholipases. Aspartic proteases, phytase, and esterase were detected in a few isolates. This study shows the reduced antifungal susceptibility and a variable production of virulence-related enzymes by Meyerozyma spp. In addition, it highlights the poor prognosis of neutropenic patients with BSI caused by this emerging species complex.

Lay Abstract

Our manuscript describes demographic, clinical and microbiological characteristics of patients with bloodstream infection by the Meyerozyma guilliermondii species complex at a reference center in oncology in Brazil.
ExoMol line lists – XXXVIII. High-temperature molecular line list of silicon dioxide (SiO2)
Authors: Owens A , Conway E K , Tennyson J , Yurchenko S N
Published: May 2020

Silicon dioxide (SiO2) is expected to occur in the atmospheres of hot rocky super-Earth exoplanets but a lack of spectroscopic data is hampering its possible detection. Here, we present the first, comprehensive molecular line list for SiO2. The line list, named OYT3, covers the wavenumber range 0 – 6000 cm−1 (wavelengths λ > 1.67 μm) and is suitable for temperatures up to T = 3000 K. Almost 33 billion transitions involving 5.69 million rotation–vibration states with rotational excitation up to J = 255 have been computed using robust first-principles methodologies. The OYT3 line list is available from the ExoMol data base at www.exomol.com.
SDSS-IV MaNGA: The kinematic-morphology of galaxies on the mass versus star-formation relation in different environments
Authors: Wang Bitao , Cappellari Michele , Peng Yingjie , Graham Mark
Published: May 2020

We study the link between the kinematic-morphology of galaxies, as inferred from integral-field stellar kinematics, and their relation between mass and star formation rate. Our sample consists of ∼3200 galaxies with integral-field spectroscopic data from the MaNGA survey (Mapping Nearby Galaxies at Apache Point Observatory) with available determinations of their effective stellar angular momentum within the half-light radius $\lambda _{R_e}$. We find that for star-forming galaxies, namely along the star formation main sequence (SFMS), the $\lambda _{R_e}$ values remain large and almost unchanged over about two orders of magnitude in stellar mass, with the exception of the lowest masses $\mathcal {M}_{\star }\lesssim 2\times 10^{9} \, \mathcal {M}_{\odot }$, where $\lambda _{R_e}$ slightly decreases. The SFMS is dominated by spiral galaxies with small bulges. Below the SFMS, but above the characteristic stellar mass $\mathcal {M}_{\rm crit}\approx 2\times 10^{11} \, \mathcal {M}_{\odot }$, there is a sharp decrease in $\lambda _{R_e}$ with decreasing star formation rate (SFR): massive galaxies well below the SFMS are mainly slow-rotator early-type galaxies, namely genuinely spheroidal galaxies without discs. Below the SFMS and below $\mathcal {M}_{\rm crit}$ the decrease of $\lambda _{R_e}$ with decreasing SFR becomes modest or nearly absent: low-mass galaxies well below the SFMS, are fast-rotator early-type galaxies, and contain fast-rotating stellar discs like their star-forming counterparts. We also find a small but clear environmental dependence for the massive galaxies: in the mass range $10^{10.9}\!-\!10^{11.5} \, \mathcal {M}_{\odot }$, galaxies in rich groups or denser regions or classified as central galaxies have lower values of $\lambda _{R_e}$. While no environmental dependence is found for galaxies of lower mass. We discuss how the above results can be understood as due to the different star formation and mass assembly histories of galaxies with varying mass.
Foreground modelling via Gaussian process regression: an application to HERA data
Authors: Ghosh Abhik , Mertens Florent , Bernardi Gianni , Santos Mário G , Kern Nicholas S , Carilli Christopher L , Grobler Trienko L , Koopmans Léon V E , Jacobs Daniel C , Liu Adrian , Parsons Aaron R , Morales Miguel F , Aguirre James E , Dillon Joshua S , Hazelton Bryna J , Smirnov Oleg M , Gehlot Bharat K , Matika Siyanda , Alexander Paul , Ali Zaki S , Beardsley Adam P , Benefo Roshan K , Billings Tashalee S , Bowman Judd D , Bradley Richard F , Cheng Carina , Chichura Paul M , DeBoer David R , Acedo Eloy de Lera , Ewall-Wice Aaron , Fadana Gcobisa , Fagnoni Nicolas , Fortino Austin F , Fritz Randall , Furlanetto Steve R , Gallardo Samavarti , Glendenning Brian , Gorthi Deepthi , Greig Bradley , Grobbelaar Jasper , Hickish Jack , Josaitis Alec , Julius Austin , Igarashi Amy S , Kariseb MacCalvin , Kohn Saul A , Kolopanis Matthew , Lekalake Telalo , Loots Anita , MacMahon David , Malan Lourence , Malgas Cresshim , Maree Matthys , Martinot Zachary E , Mathison Nathan , Matsetela Eunice , Mesinger Andrei , Neben Abraham R , Nikolic Bojan , Nunhokee Chuneeta D , Patra Nipanjana , Pieterse Samantha , Razavi-Ghods Nima , Ringuette Jon , Robnett James , Rosie Kathryn , Sell Raddwine , Smith Craig , Syce Angelo , Tegmark Max , Thyagarajan Nithyanandan , Williams Peter K G , Zheng Haoxuan
Published: May 2020

The key challenge in the observation of the redshifted 21-cm signal from cosmic reionization is its separation from the much brighter foreground emission. Such separation relies on the different spectral properties of the two components, although, in real life, the foreground intrinsic spectrum is often corrupted by the instrumental response, inducing systematic effects that can further jeopardize the measurement of the 21-cm signal. In this paper, we use Gaussian Process Regression to model both foreground emission and instrumental systematics in ∼2 h of data from the Hydrogen Epoch of Reionization Array. We find that a simple co-variance model with three components matches the data well, giving a residual power spectrum with white noise properties. These consist of an ‘intrinsic’ and instrumentally corrupted component with a coherence scale of 20 and 2.4 MHz, respectively (dominating the line-of-sight power spectrum over scales k∥ ≤ 0.2 h cMpc−1) and a baseline-dependent periodic signal with a period of ∼1 MHz (dominating over k∥ ∼ 0.4–0.8 h cMpc−1), which should be distinguishable from the 21-cm Epoch of Reionization signal whose typical coherence scale is ∼0.8 MHz.
Mode identification in three pulsating hot subdwarfs observed with TESS satellite
Authors: Sahoo S K , Baran A S , Heber U , Ostrowski J , Sanjayan S , Silvotti R , Irrgang A , Uzundag M , Reed M D , Shoaf K A , Raddi R , Vuckovic M , Ghasemi H , Zong W , Bell K J
Published: May 2020

We report on the detection of pulsations of three pulsating subdwarf B stars observed by the Transiting Exoplanet Survey Satellite (TESS) satellite and our results of mode identification in these stars based on an asymptotic period relation. SB 459 (TIC 067584818), SB 815 (TIC 169285097), and PG 0342 + 026 (TIC 457168745) have been monitored during single sectors resulting in 27 d coverage. These data sets allowed for detecting, in each star, a few tens of frequencies that we interpreted as stellar oscillations. We found no multiplets, though we partially constrained mode geometry by means of period spacing, which recently became a key tool in analyses of pulsating subdwarf B stars. Standard routine that we have used allowed us to select candidates for trapped modes that surely bear signatures of non-uniform chemical profile inside the stars. We have also done statistical analysis using collected spectroscopic and asteroseismic data of previously known subdwarf B stars along with our three stars. Making use of high precision trigonometric parallaxes from the Gaia mission and spectral energy distributions we converted atmospheric parameters to stellar ones. Radii, masses, and luminosities are close to their canonical values for extreme horizontal branch stars. In particular, the stellar masses are close to the canonical one of 0.47 M⊙ for all three stars but uncertainties on the mass are large. The results of the analyses presented here will provide important constrains for asteroseismic modelling.
An ALMA survey of the brightest sub-millimetre sources in the SCUBA-2–COSMOS field
Authors: Simpson J M , Smail Ian , Dudzevičiūtė U , Matsuda Y , Hsieh B-C , Wang W-H , Swinbank A M , Stach S M , An Fang Xia , Birkin J E , Ao Y , Bunker A J , Chapman S C , Chen Chian-Chou , Coppin K E K , Ikarashi S , Ivison R J , Mitsuhashi I , Saito T , Umehata H , Wang R , Zhao Y
Published: May 2020

We present an ALMA study of the ∼180 brightest sources in the SCUBA-2 850-μm map of the COSMOS field from the S2COSMOS survey, as a pilot study for AS2COSMOS – a full survey of the ∼1000 sources in this field. In this pilot study, we have obtained 870-μm continuum maps of an essentially complete sample of the brightest 182 sub-millimetre sources ($S_{850\, \mu \rm m}\gt $ 6.2 mJy) in COSMOS. Our ALMA maps detect 260 sub-millimetre galaxies (SMGs) spanning a range in flux density of $S_{870\, \mu \rm m}$ = 0.7–19.2 mJy. We detect more than one SMG counterpart in 34 ± 2 per cent of sub-millimetre sources, increasing to 53 ± 8 per cent for SCUBA-2 sources brighter than $S_{850\, \mu \rm m}\gt $ 12 mJy. We estimate that approximately one-third of these SMG–SMG pairs are physically associated (with a higher rate for the brighter secondary SMGs, $S_{870\, \mu \rm m}\gtrsim$ 3 mJy), and illustrate this with the serendipitous detection of bright [C ii] 157.74-μm line emission in two SMGs, AS2COS 0001.1 and 0001.2 at z = 4.63, associated with the highest significance single-dish source. Using our source catalogue, we construct the interferometric 870-μm number counts at $S_{870\, \mu \rm m}\gt $ 6.2 mJy. We use the extensive archival data of this field to construct the multiwavelength spectral energy distribution of each AS2COSMOS SMG, and subsequently model this emission with magphys to estimate their photometric redshifts. We find a median photometric redshift for the $S_{870\, \mu \rm m}\gt $ 6.2 mJy AS2COSMOS sample of z = 2.87 ± 0.08, and clear evidence for an increase in the median redshift with 870-μm flux density suggesting strong evolution in the bright end of the 870-μm luminosity function.
MUSEQuBES: calibrating the redshifts of Ly α emitters using stacked circumgalactic medium absorption profiles
Authors: Muzahid Sowgat , Schaye Joop , Marino Raffaella Anna , Cantalupo Sebastiano , Brinchmann Jarle , Contini Thierry , Wendt Martin , Wisotzki Lutz , Zabl Johannes , Bouché Nicolas , Akhlaghi Mohammad , Chen Hsiao-Wen , Claeyssens Adélaîde , Johnson Sean , Leclercq Floriane , Maseda Michael , Matthee Jorryt , Richard Johan , Urrutia Tanya , Verhamme Anne
Published: May 2020

Ly α emission lines are typically found to be redshifted with respect to the systemic redshifts of galaxies, likely due to resonant scattering of Ly α photons. Here, we measure the average velocity offset for a sample of 96 z ≈ 3.3 Ly α emitters (LAEs) with a median Ly α flux (luminosity) of ${\approx}10^{-17}~\rm erg~cm^{-2}~s^{-1}$ (${\approx}10^{42}~\rm erg~s^{-1}$) and a median star formation rate (SFR) of ≈1.3 $\rm M_{\odot }~yr^{-1}$ (not corrected for possible dust extinction), detected by the Multi-Unit Spectroscopic Explorer as part of our MUSEQuBES circumgalactic medium (CGM) survey. By postulating that the stacked CGM absorption profiles of these LAEs, probed by eight background quasars, must be centred on the systemic redshift, we measure an average velocity offset, Voffset = 171\pm 8 km s−1, between the Ly α emission peak and the systemic redshift. The observed Voffset is lower by factors of ≈1.4 and ≈2.6 compared to the velocity offsets measured for narrow-band-selected LAEs and Lyman break galaxies, respectively, which probe galaxies with higher masses and SFRs. Consistent with earlier studies based on direct measurements for individual objects, we find that the Voffset is correlated with the full width at half-maximum of the red peak of the Ly α line, and anticorrelated with the rest-frame equivalent width. Moreover, we find that Voffset is correlated with SFR with a sub-linear scaling relation, $V_{\rm offset}\propto \rm SFR^{0.16\pm 0.03}$. Adopting the mass scaling for main-sequence galaxies, such a relation suggests that Voffset scales with the circular velocity of the dark matter haloes hosting the LAEs.
Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles
Authors: Guernsey Michael W , van Kruistum Henri , Reznick David N , Pollux Bart J A , Baker Julie C
Published: May 2020

Placentation evolved many times independently in vertebrates. Although the core functions of all placentas are similar, we know less about how this similarity extends to the molecular level. Here, we study Poeciliopsis, a unique genus of live-bearing fish that have independently evolved complex placental structures at least three times. The maternal follicle is a key component of these structures. It envelops yolk-rich eggs and is morphologically simple in lecithotrophic species but has elaborate villous structures in matrotrophic species. Through sequencing, the follicle transcriptome of a matrotrophic, Poeciliopsis retropinna, and lecithotrophic, P. turrubarensis, species we found genes known to be critical for placenta function expressed in both species despite their difference in complexity. Additionally, when we compare the transcriptome of different river populations of P. retropinna, known to vary in maternal provisioning, we find differential expression of secretory genes expressed specifically in the top layer of villi cells in the maternal follicle. This provides some of the first evidence that the placental structures of Poeciliopsis function using a secretory mechanism rather than direct contact with maternal circulation. Finally, when we look at the expression of placenta proteins at the maternal–fetal interface of a larger sampling of Poeciliopsis species, we find expression of key maternal and fetal placenta proteins in their cognate tissue types of all species, but follicle expression of prolactin is restricted to only matrotrophic species. Taken together, we suggest that all Poeciliopsis follicles are poised for placenta function but require expression of key genes to form secretory villi.
Physical Constraints on Epistasis
Authors: Husain Kabir , Murugan Arvind
Published: May 2020

Living systems evolve one mutation at a time, but a single mutation can alter the effect of subsequent mutations. The underlying mechanistic determinants of such epistasis are unclear. Here, we demonstrate that the physical dynamics of a biological system can generically constrain epistasis. We analyze models and experimental data on proteins and regulatory networks. In each, we find that if the long-time physical dynamics is dominated by a slow, collective mode, then the dimensionality of mutational effects is reduced. Consequently, epistatic coefficients for different combinations of mutations are no longer independent, even if individually strong. Such epistasis can be summarized as resulting from a global nonlinearity applied to an underlying linear trait, that is, as global epistasis. This constraint, in turn, reduces the ruggedness of the sequence-to-function map. By providing a generic mechanistic origin for experimentally observed global epistasis, our work suggests that slow collective physical modes can make biological systems evolvable.
Calixa Lavallée and the Construction of a National Anthem
Authors: Duffin Ross W
Published: May 2020

Calixa Lavallée's O Canada, composed in 1880, is beloved there as the national anthem, and admired around the world. Little known today, even in his home country, Lavallée enjoyed an international career as a performer and educator, and spent many years as a “popular” musician in the United States before turning exclusively to “classical” music. This article attempts to demonstrate that, contrary to the received view of the anthem as essentially Canadian, Lavallée used his broad experience of European and American music to assemble his “chant national” from a handful of pre-existing works.
Social network analysis for social neuroscientists
Authors: Baek Elisa C , Porter Mason A , Parkinson Carolyn
Published: May 2020

Although social neuroscience is concerned with understanding how the brain interacts with its social environment, prevailing research in the field has primarily considered the human brain in isolation, deprived of its rich social context. Emerging work in social neuroscience that leverages tools from network analysis has begun to advance knowledge of how the human brain influences and is influenced by the structures of its social environment. In this paper, we provide an overview of key theory and methods in network analysis (especially for social systems) as an introduction for social neuroscientists who are interested in relating individual cognition to the structures of an individual’s social environments. We also highlight some exciting new work as examples of how to productively use these tools to investigate questions of relevance to social neuroscientists. We include tutorials to help with practical implementations of the concepts that we discuss. We conclude by highlighting a broad range of exciting research opportunities for social neuroscientists who are interested in using network analysis to study social systems.
Treatment outcomes among multidrug-resistant TB patients in Bahawal Victoria Hospital, Bahawalpur, Pakistan: a retrospective record review
Authors: Atif Muhammad , Ahmad Wajiha , Ahmad Nafees , Malik Iram , Sarwar Sajjad
Published: May 2020

Background

This study aims to evaluate the treatment outcomes and factors associated with unsuccessful treatment outcomes among multidrug-resistant TB (MDR-TB) patients.

Method

This was a retrospective observational study conducted at the Bahawal Victoria Hospital, Bahawalpur, Pakistan. The sociodemographic, clinical and treatment-related data of MDR-TB patients registered at the study site between June 2014 and December 2016 were retrospectively collected. Patients’ treatment outcomes were categorized on the basis of WHO-recommended criteria. Multivariate binary logistic regression analysis was used to find the independent factors associated with unsuccessful treatment outcomes.

Results

Out of 179 MDR-TB patients, 106 (59.2%) completed their treatment successfully. The remaining 73 patients (40.8%) had unsuccessful treatment outcomes, among whom 45 (25.1%) died, while 18 (10.1%) were lost to follow-up. Factors associated with unsuccessful treatment outcomes included age ≥40 y (AOR 4.310; p = 0.006), unsuccessful interim treatment outcomes (AOR 5.810; p = 0.032), occurrence of adverse events (AOR 0.290; p = 0.029) and ofloxacin resistance (AOR 2.952; p = 0.042).

Conclusion

The treatment success rate among the selected cohort of MDR-TB patients was less than the target of ≥75% set by the WHO in the End TB Strategy. The lower treatment success rate at the study site requires urgent attention from clinicians and program managers.
Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?
Authors: Cuypers Laura N , Baird Stuart J E , Hánová Alexandra , Locus Tatjana , Katakweba Abdul S , Gryseels Sophie , Bryja Josef , Leirs Herwig , Goüy de Bellocq Joëlle
Published: May 2020

Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.
A theoretical framework for transitioning from patient-level to population-scale epidemiological dynamics: influenza A as a case study
Authors: Hart W. S. , Maini P. K. , Yates C. A. , Thompson R. N.
Published: May 2020

Multi-scale epidemic forecasting models have been used to inform population-scale predictions with within-host models and/or infection data collected in longitudinal cohort studies. However, most multi-scale models are complex and require significant modelling expertise to run. We formulate an alternative multi-scale modelling framework using a compartmental model with multiple infected stages. In the large-compartment limit, our easy-to-use framework generates identical results compared to previous more complicated approaches. We apply our framework to the case study of influenza A in humans. By using a viral dynamics model to generate synthetic patient-level data, we explore the effects of limited and inaccurate patient data on the accuracy of population-scale forecasts. If infection data are collected daily, we find that a cohort of at least 40 patients is required for a mean population-scale forecasting error below 10%. Forecasting errors may be reduced by including more patients in future cohort studies or by increasing the frequency of observations for each patient. Our work, therefore, provides not only an accessible epidemiological modelling framework but also an insight into the data required for accurate forecasting using multi-scale models.
Topoisomerase IIα prevents ultrafine anaphase bridges by two mechanisms
Authors: Gemble Simon , Buhagiar-Labarchède Géraldine , Onclercq-Delic Rosine , Fontaine Gaëlle , Lambert Sarah , Amor-Guéret Mounira
Published: May 2020

Topoisomerase IIα (Topo IIα), a well-conserved double-stranded DNA (dsDNA)-specific decatenase, processes dsDNA catenanes resulting from DNA replication during mitosis. Topo IIα defects lead to an accumulation of ultrafine anaphase bridges (UFBs), a type of chromosome non-disjunction. Topo IIα has been reported to resolve DNA anaphase threads, possibly accounting for the increase in UFB frequency upon Topo IIα inhibition. We hypothesized that the excess UFBs might also result, at least in part, from an impairment of the prevention of UFB formation by Topo IIα. We found that Topo IIα inhibition promotes UFB formation without affecting the global disappearance of UFBs during mitosis, but leads to an aberrant UFB resolution generating DNA damage within the next G1. Moreover, we demonstrated that Topo IIα inhibition promotes the formation of two types of UFBs depending on cell cycle phase. Topo IIα inhibition during S-phase compromises complete DNA replication, leading to the formation of UFB-containing unreplicated DNA, whereas Topo IIα inhibition during mitosis impedes DNA decatenation at metaphase–anaphase transition, leading to the formation of UFB-containing DNA catenanes. Thus, Topo IIα activity is essential to prevent UFB formation in a cell-cycle-dependent manner and to promote DNA damage-free resolution of UFBs.
Oscillatory Carreau flows in straight channels
Authors: Tabakova S. , Kutev N. , Radev St.
Published: May 2020

The present paper studies the oscillatory flow of Carreau fluid in a channel at different Womersley and Carreau numbers. At high and low Womersley numbers, asymptotic expansions in small parameters, connected with the Womersley number, are developed. For the intermediate Womersley numbers, theoretical bounds for the velocity solution and its gradient, depending on the problem parameters, are proven and explicitly given. It is shown that the Carreau number changes the type of the flow velocity to be closer to the Newtonian velocity corresponding to low or high shear or to have a transitional character between both Newtonian velocities. Some numerical examples for the velocity at different Carreau and Womersley numbers are presented for illustration with respect to the similar Newtonian flow velocity.
Do pride and shame track the evaluative psychology of audiences? Preregistered replications of Sznycer
et al
. (2016, 2017)
Authors: Cohen Adam Scott , Chun Rie , Sznycer Daniel
Published: May 2020

Are pride and shame adaptations for promoting the benefits of being valued and limiting the costs of being devalued, respectively? Recent findings indicate that the intensities of anticipatory pride and shame regarding various potential acts and traits track the degree to which fellow community members value or disvalue those acts and traits. Thus, it is possible that pride and shame are engineered to activate in proportion to others' valuations. Here, we report the results of two preregistered replications of the original pride and shame reports (Sznycer
et al.
2016
Proc. Natl Acad. Sci. USA
113
, 2625–2630. (
doi:10.1073/pnas.1514699113
); Sznycer
et al
. 2017
Proc. Natl Acad. Sci. USA
114
, 1874–1879. (
doi:10.1073/pnas.1614389114
)). We required the data to meet three criteria, including frequentist and Bayesian replication measures. Both replications met the three criteria. This new evidence invites a shifting of prior assumptions about pride and shame: these emotions are engineered to gain the benefits of being valued and avoid the costs of being devalued.
Reversible morphological changes in a juvenile marine fish after exposure to predatory alarm cues
Authors: Díaz-Gil Carlos , Alós Josep , Arechavala-Lopez Pablo , Palmer Miquel , Riera-Batle Inmaculada , Grau Amalia , Catalán Ignacio A.
Published: May 2020

Chemical cues from predators induce a range of predator-induced morphological defences (PIMDs) observed across fish taxa. However, the mechanisms, consistency, direction and adaptive value of PIMDs are still poorly studied. Here, we have tested if predatory cues can induce changes in the body shape of the juvenile marine fishSparus auratareared under controlled conditions without the presence of predators by exposing individuals to the olfactory stimulus of a fish predator. We tested our hypothesis using a nested replicated before-after-control-impact experiment, including recovery (potential reversibility) after the cessation of the predator stimulus. Differences in the size-independent body shape were explored using landmark-based geometric morphometrics and revealed that, on average, individuals exposed to a predatory cue presented deeper bodies and longer caudal regions, according to our adaptive theoretical predictions. These average plastic responses were reversible after withdrawal of the stimulus and individuals returned to average body shapes. We, therefore, provide evidence supporting innate reversible PIMDs in marine naive fish reared under controlled conditions. The effects at the individual level, including fitness and the associated applied implications, deserve further research.
Diffuse retro-reflective imaging for improved video tracking of mosquitoes at human baited bednets
Authors: Voloshin Vitaly , Kröner Christian , Seniya Chandrabhan , Murray Gregory P. D. , Guy Amy , Towers Catherine E. , McCall Philip J. , Towers David P.
Published: May 2020

Robust imaging techniques for tracking insects have been essential tools in numerous laboratory and field studies on pests, beneficial insects and model systems. Recent innovations in optical imaging systems and associated signal processing have enabled detailed characterization of nocturnal mosquito behaviour around bednets and improvements in bednet design, a global essential for protecting populations against malaria. Nonetheless, there remain challenges around ease of use for large-scale
in situ
recordings and extracting data reliably in the critical areas of the bednet where the optical signal is attenuated. Here, we introduce a retro-reflective screen at the back of the measurement volume, which can simultaneously provide diffuse illumination, and remove optical alignment issues while requiring only one-sided access to the measurement space. The illumination becomes significantly more uniform, although noise removal algorithms are needed to reduce the effects of shot noise, particularly across low-intensity bednet regions. By systematically introducing mosquitoes in front of and behind the bednet in laboratory experiments, we are able to demonstrate robust tracking in these challenging areas. Overall, the retro-reflective imaging set-up delivers mosquito segmentation rates in excess of 90% compared to less than 70% with backlit systems.
Mathematical modelling of the role of GADD45β in the pathogenesis of multiple myeloma
Authors: Zhang Yao , Zhen Changqing , Yang Qing , Ji Bing
Published: May 2020

Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β
-
and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.