bluuebunny/crossref_metadata_2025 huggingface dataset:
Local in Time Strichartz Estimates for the Dirac Equation on Spherically Symmetric Spaces
Authors: Cacciafesta Federico , de Suzzoni Anne-Sophie
Published: July 2020

We prove local in time Strichartz estimates for the Dirac equation on spherically symmetric manifolds. As an application, we give a result of local well-posedness for some nonlinear models.
Inverse Steklov Spectral Problem for Curvilinear Polygons
Authors: Krymski Stanislav , Levitin Michael , Parnovski Leonid , Polterovich Iosif , Sher David A
Published: July 2020

This paper studies the inverse Steklov spectral problem for curvilinear polygons. For generic curvilinear polygons with angles less than $\pi $, we prove that the asymptotics of Steklov eigenvalues obtained in [ 20] determines, in a constructive manner, the number of vertices and the properly ordered sequence of side lengths, as well as the angles up to a certain equivalence relation. We also present counterexamples to this statement if the generic assumptions fail. In particular, we show that there exist non-isometric triangles with asymptotically close Steklov spectra. Among other techniques, we use a version of the Hadamard–Weierstrass factorization theorem, allowing us to reconstruct a trigonometric function from the asymptotics of its roots.
Crystal structure of the ternary complex of TCR, MHC class I and lipopeptides
Authors: Morita Daisuke , Iwashita Chieri , Mizutani Tatsuaki , Mori Naoki , Mikami Bunzo , Sugita Masahiko
Published: July 2020

The covalent conjugation of a 14-carbon fatty acid (myristic acid) to the N-terminal Gly residue, termed N-myristoylation, occurs in some viral proteins to dictate their pathological function. This protein lipidation reaction, however, is monitored by host cytotoxic T lymphocytes that are capable of recognizing N-terminal lipopeptide fragments in the context of major histocompatibility complex (MHC) class I molecules. In a rhesus model of human AIDS, for example, the classical MHC class I allomorph, Mamu-B*05104, was shown to bind SIV Nef-derived 4-mer lipopeptides (myristic acid-Gly-Gly-Ala-Ile; C14nef4) and present them to the CD8+ T-cell line, SN45. These lipopeptides accommodated in MHC class I molecules expose much shorter peptide chains than conventional MHC class I-presented 8–10-mer peptides, and the molecular mechanisms by which αβ T-cell receptors (TCRs) recognize lipopeptides currently remain unclear. An X-ray crystallographic analysis of the SN45 TCR α and β heterodimer in a form that was co-crystallized with the C14nef4-bound Mamu-B*05104 complex indicated that the amide group of the N-myristoylated glycine residue offered a primary T-cell epitope by establishing a sole hydrogen bond between its nitrogen atom and the side chain of Glu at position 101 of CDR3β. Accordingly, the Glu to Ala mutation at this position resulted in the loss of lipopeptide recognition. On the other hand, TCRs were positioned remotely from the peptide portion of C14nef4, and strong interactions were not observed. Thus, these observations provide novel structural insights into lipopeptide recognition by TCRs, which contrast sharply with the general molecular principle of peptide recognition.
Activity of cefepime/zidebactam against MDR Escherichia coli isolates harbouring a novel mechanism of resistance based on four-amino-acid inserts in PBP3
Authors: Bhagwat Sachin S , Hariharan Periasamy , Joshi Prashant R , Palwe Snehal R , Shrivastava Rahul , Patel Mahesh V , Devanga Ragupathi Naveen Kumar , Bakthavatchalam Yamuna Devi , Ramesh Mayur S , Soman Rajeev , Veeraraghavan Balaji
Published: July 2020

Background

Recent reports reveal the emergence of Escherichia coli isolates harbouring a novel resistance mechanism based on four-amino-acid inserts in PBP3. These organisms concomitantly expressed ESBLs or/and serine-/metallo-carbapenemases and were phenotypically detected by elevated aztreonam/avibactam MICs.

Objectives

The in vitro activities of the investigational antibiotic cefepime/zidebactam and approved antibiotics (ceftazidime/avibactam, ceftolozane/tazobactam, imipenem/relebactam and others) were determined against E. coli isolates harbouring four-amino-acid inserts in PBP3.

Methods

Whole-genome sequenced E. coli isolates (n = 89) collected from a large tertiary care hospital in Southern India (n = 64) and from 12 tertiary care hospitals located across India (n = 25) during 2016–18, showing aztreonam/avibactam MICs ≥1 mg/L (≥4 times the aztreonam epidemiological cut-off) were included in this study. The MICs of antibiotics were determined using the reference broth microdilution method.

Results

Four-amino-acid inserts [YRIK (n = 30) and YRIN (n = 53)] were found in 83/89 isolates. Among 83 isolates, 65 carried carbapenemase genes [blaNDM (n = 39), blaOXA-48-like (n = 11) and blaNDM + blaOXA-48-like (n = 15)] and 18 isolates produced ESBLs/class C β-lactamases only. At least 16 unique STs were noted. Cefepime/zidebactam demonstrated potent activity, with all isolates inhibited at ≤1 mg/L. Comparator antibiotics including ceftazidime/avibactam and imipenem/relebactam showed limited activities.

Conclusions

E. coli isolates concurrently harbouring four-amino-acid inserts in PBP3 and NDM are an emerging therapeutic challenge. Assisted by the PBP2-binding action of zidebactam, the cefepime/zidebactam combination overcomes both target modification (PBP3 insert)- and carbapenemase (NDM)-mediated resistance mechanisms in E. coli.
Antimicrobial Stewardship Optimization in the Emergency Department: The Effect of Multiplex Respiratory Pathogen Testing and Targeted Educational Intervention
Authors: Durant Thomas J S , Kubilay Nejla Zeynep , Reynolds Jesse , Tarabar Asim F , Dembry Louise M , Peaper David R
Published: July 2020

Background

Antibacterial agents are often prescribed for patients with suspected respiratory tract infections even though these are most often caused by viruses. In this study, we sought to evaluate the effect of Respiratory Pathogen Panel (RPP) PCR result availability and antimicrobial stewardship education on antibiotic prescription rates in the adult emergency department (ED).

Methods

We compared rates of antibacterial and oseltamivir prescriptions between 2 nonconsecutive influenza seasons among ED visits, wherein the latter season followed the implementation of a comprehensive educational stewardship campaign. In addition, we sought to elucidate the effect of RPP-PCR on antibiotic prescriptions, with focus on result availability prior to the conclusion of emergency department encounters.

Results

Antibiotic prescription rates globally decreased by 17.9% in the FS-17/18 cohort compared to FS-14/15 (P < 0.001), while oseltamivir prescription rates stayed the same overall (P = 0.42). Multivariate regression across both cohorts revealed that patients were less likely to receive antibiotics if RPP-PCR results were available before the end of the ED visit or if the RPP-PCR result was positive for influenza. Patients in the educational intervention cohort were also less likely to receive an antibiotic prescription.

Conclusion

This study provides evidence that RPP-PCR results are most helpful if available prior to the end of the provider-patient interaction. Further, these data suggest that detection of influenza remains an influential result in the context of antimicrobial treatment decision making. In addition, these data contribute to the body of literature which supports comprehensive ASP interventions including leadership and patient engagement.
Colostrum composition and immunoglobulin G content in dairy and dual-purpose cattle breeds
Authors: Kessler Evelyne C , Bruckmaier Rupert M , Gross Josef J
Published: July 2020

Immunoglobulins (Ig) are essential components in the colostrum of bovine species that enable passive immunization of newborn calves. Concentrations of fat and protein are greater in colostrum compared with mature milk and represent a vital source of energy and nutrients. Colostral IgG was shown to vary between individual dairy cows, but comparative data on different breeds and performance levels are scarce. The objective of the present field study was to investigate the contents of total IgG, fat, protein, and lactose in colostrum in different Swiss and German dairy and dual-purpose breeds. We collected colostrum samples of 458 cows of 13 different breeds (dairy breeds: Brown Swiss, Swiss and German Holstein Friesian, and New Zealand Holstein; dual-purpose breeds: German Fleckvieh, Holstein Friesian × Montbéliarde, Montbéliarde, Murnau-Werdenfels, Original Braunvieh, Pinzgauer, Rhetic Gray, and Simmental; and beef-type crossbred: Charolais × Holstein Friesian). Colostrum samples were obtained between 5 and 900 min after calving and analyzed for total IgG, fat protein, and lactose contents. Immunoglobulin G concentrations varied between 12.7 and 204.0 mg/mL. No effect of breeding purpose (i.e., dairy or dual-purpose) nor of previous lactation yield on IgG content was observed. However, milking of cows for the first time later than 12 h after parturition resulted in lower colostrum IgG concentrations compared with colostrum harvest within 9 h after calving (P < 0.05). Multiparous cows had a higher colostral IgG concentration than primiparous cows (P < 0.0001). Overall, concentrations of IgG and other constituents in colostrum varied widely in the different cattle breeds. High-yielding dairy cows did not have poorer colostrum quality compared with lower-yielding animals or beef and dual-purpose breeds, which suggests an individually different transfer of circulating IgG into colostrum.
Attracting Chrysopidae With Plant Volatiles for Lace Bug (Hemiptera: Tingidae) Control in Rhododendrons and Azaleas
Authors: Graham Katerina Velasco , Choi Man-Yeon , Lee Jana C
Published: July 2020

The azalea lace bug (Stephanitis pyrioides Scott) (Hemiptera: Tingidae) is an invasive pest of rhododendrons and azaleas (Ericaceae: Rhododendron), which feeds on the underside of leaves causing chlorosis, reduced photosynthesis, and even plant death. While insecticides can control this pest, growers, landscape managers, and homeowners have requested softer alternatives. Augmentative release of predatory green lacewing Chrysoperla sp. (Neuroptera: Chrysopidae) eggs and larvae has reduced S. pyrioides, but large-scale implementation may not be practical nor cost-effective. Attracting naturally occurring Chrysopidae with plant volatiles may be an economical and convenient option. In this study, we tested whether volatile blends 1) attracted Chrysoperla sp., and 2) controlled S. pyrioides populations on Rhododendron spp. in farm or urban landscapes. Experimental plots contained different multicomponent lures placed aboveground next to infested plants. Adult Chrysoperla sp., other natural enemies, and S. pyrioides from egg to adult stages were monitored in both farm and urban landscapes for two summers. Overall, two out of three volatile blends consistently attracted Chrysoperla sp. to sticky traps near baited plants. Methyl salicylate + acetic acid + 2-phenylethanol (methyl salicylate blend) and acetophenone + acetic acid + 2-phenylethanol (acetophenone blend) captured more adult Chrysoperla sp. than control traps in farm landscapes. However, only the acetophenone blend was associated with a slight reduction of S. pyrioides. Additional research is needed to determine whether the phenology of the first generation of both species are synchronized for effective season biological control in the Pacific Northwest.
Molecular Diagnosis and Prevalence of Trypanosoma vivax (Trypanosomatida: Trypanosomatidae) in Buffaloes and Ectoparasites in the Brazilian Amazon Region
Authors: Dyonisio Gustavo Henrique Souza , Batista Helder Ribeiro , da Silva Ryan Emiliano , Azevedo Roberta Carvalho de Freitas e , Costa Jaciara de Oliveira Jorge , Manhães Ingridi Braz de Oliveira , Tonhosolo Renata , Gennari Solange Maria , Minervino Antonio Humberto Hamad , Marcili Arlei
Published: July 2020

Trypanosoma vivax Ziemann is a parasite that affects both wild and domestic ungulates and is transmitted mechanically via tabanids and other blood-sucking insects in the Americas. A total of 621 blood samples from water buffaloes (Bubalus bubalis (Linnaeus) (Artiodactyla: Bovidae), and 184 ectoparasite samples (Amblyomma cajennense (Fabricius) sensu stricto and Rhipicephalus (Boophilus) microplus (Canestrini) (Acari: Ixodidae), and Haematopinus tuberculatus (Burmeister) (Phthiraptera: Haematopinidae)) were obtained from 60 farms in the State of Pará, Brazilian Amazon. Twelve buffalo blood samples (1.89%) and 11 ectoparasites (6%) were positive for T. vivax based on the cathepsin L-like gene. All sequences were 99% similar to T. vivax from northeastern Brazil (EU753788) in amplified PCR assays on each of the hosts tested.
Comparison of prostate verification with implanted gold markers in tissue surrounding the prostate and pelvic bony anatomy for external beam radiation therapy following low-dose-rate brachytherapy: a prospective clinical trial
Authors: Kaneda Tomoya , Ohashi Toshio , Hanada Takashi , Takenaka Koji , Nishimura Shuichi , Sakayori Masanori , Sutani Shinya , Momma Tetsuo , Shigematsu Naoyuki
Published: July 2020

We aimed to investigate whether gold marker implantation in the tissue surrounding the prostate could accurately monitor setup errors during external beam radiation therapy (EBRT) following low-dose-rate (LDR) brachytherapy. Thirty-eight patients had confirmed intermediate- or high-risk prostate cancer and received EBRT following LDR brachytherapy. In >175 computed tomography imaging sessions, the average values of the weekly setup error during EBRT to the prostate centroid at the time of gold marker matching in the surrounding tissue of the prostate and pelvic bone matching were measured and then compared using the Wilcoxon signed-rank test. Gold marker matching in the surrounding tissue of the prostate estimated setup errors better than those estimated by bone matching (3D displacement = 2.7 ± 2.0 vs 3.8 ± 2.6 mm, P < 0.01). Overall, the standard deviation of systematic (Σ) and random (σ) setup error was lower with gold marker matching than with bone matching (3D displacement = 1.8 and 1.1 mm vs 2.1 and 1.6 mm, respectively). With gold marker matching, the setup error of the position of the prostate centroid was smaller, and the optimal setup margin was lower than that with bone matching (2Σ + 0.7σ and 2.5Σ + 0.7σ of 3D displacement = 4.3 and 5.2 mm vs 5.3 and 6.4 mm, respectively). This high-precision radiotherapy approach placing gold markers in the surrounding tissue of the prostate can allow more accurate setup during EBRT following LDR brachytherapy.
Combined effects of cisplatin and photon or proton irradiation in cultured cells: radiosensitization, patterns of cell death and cell cycle distribution
Authors: Iwata Hiromitsu , Shuto Tsuyoshi , Kamei Shunsuke , Omachi Kohei , Moriuchi Masataka , Omachi Chihiro , Toshito Toshiyuki , Hashimoto Shingo , Nakajima Koichiro , Sugie Chikao , Ogino Hiroyuki , Kai Hirofumi , Shibamoto Yuta
Published: July 2020

The purpose of the current study was to investigate the biological effects of protons and photons in combination with cisplatin in cultured cells and elucidate the mechanisms responsible for their combined effects. To evaluate the sensitizing effects of cisplatin against X-rays and proton beams in HSG, EMT6 and V79 cells, the combination index, a simple measure for quantifying synergism, was estimated from cell survival curves using software capable of performing the Monte Carlo calculation. Cell death and apoptosis were assessed using live cell fluorescence imaging. HeLa and HSG cells expressing the fluorescent ubiquitination-based cell cycle indicator system (Fucci) were irradiated with X-rays and protons with cisplatin. Red and green fluorescence in the G1 and S/G2/M phases, respectively, were evaluated and changes in the cell cycle were assessed. The sensitizing effects of ≥1.5 μM cisplatin were observed for both X-ray and proton irradiation (P < 0.05). In the three cell lines, the average combination index was 0.82–1.00 for X-rays and 0.73–0.89 for protons, indicating stronger effects for protons. In time-lapse imaging, apoptosis markedly increased in the groups receiving ≥1.5 μM cisplatin + protons. The percentage of green S/G2/M phase cells at that time was higher when cisplatin was combined with proton beams than with X-rays (P < 0.05), suggesting more significant G2 arrest. Proton therapy plus ≥1.5 μM cisplatin is considered to be very effective. When combined with cisplatin, proton therapy appeared to induce greater apoptotic cell death and G2 arrest, which may partly account for the difference observed in the combined effects.
Reinforcing and contesting neoliberal citizenship: Legal advocates and the asylum interview at the US–Mexico border
Authors: Riva Sara , Routon Erin
Published: July 2020

This article explores the mechanisms in which, through the US family detention asylum process, neoliberal ideas of citizenship are reinforced and contested. Through ethnographic research, and using a Foucauldian lens, we take a closer look at the neoliberal processes involved within so-called family detention. Specifically, we focus on legal advocates who are helping detained women prepare for their legal interviews. This paper argues that humanitarian aid work becomes knowable through attention to microlevel details and forms of practice—on the ground and at the margins. This affords a recognition of not only areas of functional solidarity or symbiosis with the state, but also those less visible forms of contestation. We claim that while legal advocates play a role within the neoliberal regimes at work inside these centres, they also contest this system in various critical ways, ensuring both access to legal representation for all detainees and their eventual release.
Irreconcilable Loss, Avoidance, and Hypervigilance: Facilitators of Refugee-Specific Posttraumatic Growth
Authors: McCormack Lynne , Strezov James
Published: July 2020

Few studies explore both positive and negative interpretations of life as a refugee despite an abundance of literature that recognizes psychological growth as an outcome of adversity. This iterative phenomenological study sought positive and negative subjective interpretations from five former adult refugees. Data were collected through semi-structured interviews and analyzed using Interpretative Phenomenological Analysis. One superordinate theme, authentic self in the irreconcilable loss of refugee trauma, overarched four subordinate themes, refugee trauma, refugeeism, life is a gift, and authenticity in posttraumatic growth, which mapped the participants’ journeys from hopelessness and fear, to a determined rediscovery of ‘self’. Rather than avoidance and hypervigilent behaviours representing psychological pathology, these participants used both behaviours as coping strategies for reconciling the traumatic loss of family and familial support, culture, country, financial and social stability, and security as a refugee, recognizing the need to welcome a future out of a past that could not be reconciled.
Limitations of the Right to Have Rights: The Case of Denmark
Authors: Bell Nathan
Published: July 2020

The growing dimensions of the global refugee crisis have led to considerable attention being paid by theorists to Hannah Arendt’s notion of the ‘right to have rights’ (RTHR), concerning the right to asylum. There is a historical asylum case which Arendt privileged as exemplary, in relation to both asylum and political action: the refuge provided by Denmark for its Jewish citizens, and some Jewish refugees, during the Second World War. I argue that reading Arendt’s reflections on the RTHR alongside her writings on the Denmark case provides greater illumination of both. The scope of the rescue of Jewish people in Denmark is arguably not as laudable as Arendt maintained, as Denmark placed restrictions upon the entry of refugees into its territory. This critique reconfigures the import of the RTHR in relation to Arendt’s writings on plurality as the ‘law of the earth’.
Geographical Trajectories of Refugees in Sweden: Uncovering Patterns and Drivers of Inter-Regional (Im)mobility
Authors: Vogiazides Louisa , Mondani Hernan
Published: July 2020

Many countries actively seek to disperse refugees to counteract residential segregation or/and take measures to attract and retain international migrants in smaller communities to mitigate or reverse population decline. This study explores the regional distribution and inter-regional mobility among refugees in Sweden. It uses individual-level register data to follow two cohorts for 8 years after their arrival in Sweden, distinguishing between refugees subject to a placement policy in the 1990s and recent cohorts that either had arranged their own housing or had been assigned housing. It uses sequence analysis and multinomial logit regression to analyse regional trajectories, and event history analysis to examine mobility determinants. The results indicate that most refugees remained in the same type of region throughout the period. A significant proportion of refugees with assigned housing in large city or small city/rural regions stayed there over a long period, suggesting that refugee settlement policies have long-lasting consequences.
The Media and Displacements: News Frames of Victims of Herders/Farmers Conflict in Nigeria
Authors: Oyeoku Eke Kalu , Gever Verlumun Celestine , Alu Nkem Fortunes , Ukpai Eke N , Obikwelu Chizoba , Onuora Chijioke Noel
Published: July 2020

This study examined media framing of internally displaced persons (IDPs) of the conflict between farmers and herdsmen in Nigeria. In doing so, particular attention was paid to source, frames, language, and solution suggested. The researchers adopted a mixed method of content analysis and structured interview. Therefore, a total of 279 newspaper stories, 161 TV stories, and 47 radio stories were examined for duration of 4 years. Also, a total of 20 journalists were interviewed for the study. In the area of theory, the study used framing theory to ground the study. Data from content analysis of the news frames were handled statistically, while descriptive and inferential statistics were used only as tools for organizing, summarizing, and presenting the empirical data. Data from oral interviews were handled using thematic analysis. Result showed that the framing of IDPs differs across the different media examined.
Peritonitis from perforated sigmoid mass as the first manifestation of metastatic squamous cell lung cancer: a case report and review of literature
Authors: Chandra Raghav , Dogeas Epameinondas , Nevarez Nicole , Augustine Mathew , Huerta Sergio
Published: July 2020

Lung cancer (LC) is an aggressive malignancy with early metastatic spread and poor prognosis. Gastrointestinal metastases from primary LC are extremely rare with highly variable presentations. In this report, we review the case of a patient who presented with peritonitis secondary to perforated sigmoid mass as the first manifestation of metastatic squamous cell LC.
CaASR1 promotes salicylic acid- but represses jasmonic acid-dependent signaling to enhance the resistance of Capsicum annuum to bacterial wilt by modulating CabZIP63
Authors: Huang Jinfeng , Shen Lei , Yang Sheng , Guan Deyi , He Shuilin
Published: July 2020

CabZIP63 acts positively in the resistance of pepper (Capsicum annuum) to bacterial wilt caused by Ralstonia solanacearum or tolerance to high-temperature/high-humidity stress, but it is unclear how CabZIP63 achieves its functional specificity against R. solanacearum. Here, CaASR1, an abscisic acid-, stress-, and ripening-inducible protein of C. annuum, was functionally characterized in modulating the functional specificity of CabZIP63 during the defense response of pepper to R. solanacearum. In pepper plants inoculated with R. solanacearum, CaASR1 was up-regulated before 24 h post-inoculation but down-regulated thereafter, and was down-regulated by high-temperature/high-humidity stress. Data from gene silencing and transient overexpression experiments indicated that CaASR1 acts as a positive regulator in the immunity of pepper against R. solanacearum and a negative regulator of thermotolerance. Pull-down combined with mass spectrometry revealed that CaASR1 interacted with CabZIP63 upon R. solanacearum infection; the interaction was confirmed by microscale thermophoresis and bimolecular fluorescence complementation assays.CaASR1 silencing upon R. solanacearum inoculation repressed CabZIP63-mediated transcription from the promoters of the salicylic acid (SA)-dependent CaPR1 and CaNPR1, but derepressed transcription of CaHSP24 and the jasmonic acid (JA)-dependent CaDEF1. Our findings suggest that CaASR1 acts as a positive regulator of the defense response of pepper to R. solanacearum by interacting with CabZIP63, enabling it to promote SA-dependent but repress JA-dependent immunity and thermotolerance during the early stages of infection.
Nutrition-mediated cell and tissue-level anatomy triggers the covariation of leaf photosynthesis and leaf mass per area
Authors: Lu Zhifeng , Ren Tao , Li Jing , Hu Wenshi , Zhang Jianglin , Yan Jinyao , Li Xiaokun , Cong Rihuan , Guo Shiwei , Lu Jianwei
Published: July 2020

Plants in nutrient-poor habitats converge towards lower rates of leaf net CO2 assimilation (Aarea); however, they display variability in leaf mass investment per area (LMA). How a plant optimizes its leaf internal carbon investment may have knock-on effects on structural traits and, in turn, affect leaf carbon fixation. Quantitative models were applied to evaluate the structural causes of variations in LMA and their relevance to Aarea in rapeseed (Brassica napus) based on their responses to nitrogen (N), phosphorus (P), potassium (K), and boron (B) deficiencies. Leaf carbon fixation decreased in response to nutrient deficiency, but the photosynthetic limitations varied greatly depending on the deficient nutrient. In comparison with Aarea, the LMA exhibited diverse responses, being increased under P or B deficiency, decreased under K deficiency, and unaffected under N deficiency. These variations were due to changes in cell- and tissue-level carbon investments between cell dry mass density (N or K deficiency) and cellular anatomy, including cell dimension and number (P deficiency), or both (B deficiency). However, there was a conserved pattern independent of nutrient-specific limitations—low nutrient availability reduced leaf carbon fixation but increased carbon investment in non-photosynthetic structures, resulting in larger but fewer mesophyll cells with a thicker cell wall but a lower chloroplast surface area appressed to the intercellular airspace, which reduced the mesophyll conductance and feedback-limited Aarea. Our results provide insight into the importance of mineral nutrients in balancing the leaf carbon economy by coordinating leaf carbon assimilation and internal distribution.
The Te[N ii]–Te[O iii] temperature relation in H ii regions and the reliability of strong-line methods
Authors: Arellano-Córdova K Z , Rodríguez M
Published: July 2020

We use a sample of 154 observations of 124 H ii regions that have measurements of both Te[O iii] and Te[N ii], compiled from the literature, to explore the behaviour of the Te[O iii]–Te[N ii] temperature relation. We confirm that the relation depends on the degree of ionization and present a new set of relations for two different ranges of this parameter. We study the effects introduced by our temperature relations and four other available relations in the calculation of oxygen and nitrogen abundances. We find that our relations improve slightly on the results obtained with the previous ones. We also use a sample of 26 deep, high-resolution spectra to estimate the contribution of blending to the intensity of the temperature-sensitive line [O iii] λ4363, and we derive a relation to correct Te[O iii] for this effect. With our sample of 154 spectra, we analyse the reliability of the R, S, O3N2, N2, ONS, and C strong-line methods by comparing the metallicity obtained with these methods with the one implied by the direct method. We find that the strong-line methods introduce differences that reach ∼0.2 dex or more, and that these differences depend on O/H, N/O, and the degree of ionization.
The turbulence driving parameter of molecular clouds in disc galaxies
Authors: Körtgen Bastian
Published: July 2020

Supersonic turbulence plays a pivotal role during the formation of molecular clouds and stars in galaxies. However, little is known about how the fraction of compressive and solenoidal modes in the velocity field evolves over time and how it depends on properties of the molecular cloud or the galactic environment. In this work, we carry out magnetohydrodynamical simulations of disc galaxies and study the time evolution of the turbulence driving parameter for an ensemble of clouds. We find that the time-averaged turbulence driving parameter is insensitive to the position of the cloud within the galaxy. The ensemble-averaged driving parameter is found to be rather compressive with b ∼ 0.5–0.7, indicating almost time-independent global star formation properties. However, each individual cloud shows a highly fluctuating driving parameter, which would strongly affect the cloud’s star formation rate. We find that the mode of turbulence driving can rapidly change within only a few Myr, both from solenoidal to compressive and vice versa. We attribute these changes to cloud collisions and to tidal interactions with clouds or overdensities in the environment. Last, we find no significant differences in the average driving parameter between hydrodynamic and initially strongly magnetized galaxies. However, the magnetic field tends to reduce the overall fluctuation of the driving parameter. The average driving and its uncertainty are seen to be in agreement with recent constraints on the turbulence driving mode for solar neighbourhood clouds.
Estimating supermassive black hole masses in active galactic nuclei using polarization of broad Mg ii, H α, and H β lines
Authors: Savić Đorđe , Popović L Č , Shablovinskaya E , Afanasiev V L
Published: July 2020

For type-1 active galactic nuclei (AGNs) for which the equatorial scattering is the dominant broad-line polarization mechanism, it is possible to measure the supermassive black hole (SMBH) mass by tracing the Keplerian motion across the polarization plane position angle φ. So far, this method has been used for 30 objects but only for H α emission line. We explore the possibilities of this method for determining SMBH masses using polarization in broad emission lines by applying it for the first time to Mg ii λ2798 Å spectral line. We use three-dimensional (3-D) Monte Carlo radiative transfer code stokes for simultaneous modelling of equatorial scattering of H α, H β, and Mg ii lines. We included vertical inflows and outflows in the Mg ii broad-line region (BLR). We find that polarization states of H α and H β lines are almost identical and SMBH-mass estimates differ by 7 per cent. For Mg ii line, we find that φ exhibits an additional ‘plateau’ with a constant φ, which deviates than the profiles expected for pure Keplerian motion. SMBH-mass estimates using Mg ii line are higher by up to 35 per cent than those obtained from H α and H β lines. Our model shows that for vertical inflows and outflows in the BLR that are higher or comparable to the Keplerian velocity, this method can be applied as a first approximation for obtaining SMBH mass.
Detection of very-high-energy gamma-ray transients with monitoring facilities
Authors: La Mura G , Chiaro G , Conceição R , De Angelis A , Pimenta M , Tomé B
Published: July 2020

The observation of very-high-energy γ-rays (VHE γ-rays, $E \gt 100\,$ GeV) has ledto the identification of extremely energetic processes and particle-acceleration sites both within our Galaxy and beyond. It is expected that VHE facilities, such as the Cherenkov Telescope Array, will explore these sources with an unprecedented level of detail. However, the transient and unpredictable nature of many important processes means that their observation requires the development of proper monitoring strategies. In this study, we estimate the properties of VHE transients that can be effectively detected by monitoring facilities. We use data collected by the Fermi-LAT instrument during its monitoring campaign to select events that are probably associated with VHE emission. We use this sample to estimate the frequency, the luminosity and the time-scales of various transients, focusing on blazar flares and gamma-ray bursts. We discuss how the balance between the field of view, sensitivity and duty cycle of an observatory affects the likelihood of detecting transients that occur at the inferred rates, and we conclude by describing the contribution that current and near-future monitoring facilities can make to the identification and study of VHE transient emission.
The diversity and variability of star formation histories in models of galaxy evolution
Authors: Iyer Kartheik G , Tacchella Sandro , Genel Shy , Hayward Christopher C , Hernquist Lars , Brooks Alyson M , Caplar Neven , Davé Romeel , Diemer Benedikt , Forbes John C , Gawiser Eric , Somerville Rachel S , Starkenburg Tjitske K
Published: July 2020

Understanding the variability of galaxy star formation histories (SFHs) across a range of time-scales provides insight into the underlying physical processes that regulate star formation within galaxies. We compile the SFHs of galaxies at z = 0 from an extensive set of models, ranging from cosmological hydrodynamical simulations (Illustris, IllustrisTNG, Mufasa, Simba, EAGLE), zoom simulations (FIRE-2, g14, and Marvel/Justice League), semi-analytic models (Santa Cruz SAM) and empirical models (UniverseMachine), and quantify the variability of these SFHs on different time-scales using the power spectral density (PSD) formalism. We find that the PSDs are well described by broken power laws, and variability on long time-scales (≳1 Gyr) accounts for most of the power in galaxy SFHs. Most hydrodynamical models show increased variability on shorter time-scales (≲300 Myr) with decreasing stellar mass. Quenching can induce ∼0.4−1 dex of additional power on time-scales >1 Gyr. The dark matter accretion histories of galaxies have remarkably self-similar PSDs and are coherent with the in situ star formation on time-scales >3 Gyr. There is considerable diversity among the different models in their (i) power due to star formation rate variability at a given time-scale, (ii) amount of correlation with adjacent time-scales (PSD slope), (iii) evolution of median PSDs with stellar mass, and (iv) presence and locations of breaks in the PSDs. The PSD framework is a useful space to study the SFHs of galaxies since model predictions vary widely. Observational constraints in this space will help constrain the relative strengths of the physical processes responsible for this variability.
An uncertainty principle for star formation – V. The influence of dust extinction on star formation rate tracer lifetimes and the inferred molecular cloud lifecycle
Authors: Haydon Daniel T , Fujimoto Yusuke , Chevance Mélanie , Kruijssen J M Diederik , Krumholz Mark R , Longmore Steven N
Published: July 2020

Recent observational studies aiming to quantify the molecular cloud lifecycle require the use of known ‘reference time-scales’ to turn the relative durations of different phases of the star formation process into absolute time-scales. We previously constrained the characteristic emission time-scales of different star formation rate (SFR) tracers, as a function of the SFR surface density and metallicity. However, we omitted the effects of dust extinction. Here, we extend our suite of SFR tracer emission time-scales by accounting for extinction, using synthetic emission maps of a high-resolution hydrodynamical simulation of an isolated, Milky Way-like disc galaxy. The stellar feedback included in the simulation is inefficient compared to observations, implying that it represents a limiting case in which the duration of embedded star formation (and the corresponding effect of extinction) is overestimated. Across our experiments, we find that extinction mostly decreases the SFR tracer emission time-scale, changing the time-scales by factors of 0.04–1.74, depending on the gas column density. UV filters are more strongly affected than H α filters. We provide the limiting correction factors as a function of the gas column density and flux sensitivity limit for a wide variety of SFR tracers. Applying these factors to observational characterizations of the molecular cloud lifecycle produces changes that broadly fall within the quoted uncertainties, except at high kpc-scale gas surface densities ($\Sigma _{\rm g}\gtrsim 20~{\mathrm{M_{\odot }\, pc^{-2}}}$). Under those conditions, correcting for extinction may decrease the measured molecular cloud lifetimes and feedback time-scales, which further strengthens previous conclusions that molecular clouds live for a dynamical time and are dispersed by early, pre-supernova feedback.
Constraining the oblateness of transiting planets with photometry and spectroscopy
Authors: Akinsanmi B , Barros S C C , Santos N C , Oshagh M , Serrano L M
Published: July 2020

Rapid planetary rotation can cause the equilibrium shape of a planet to be oblate. While planetary oblateness has mostly been probed by examining the subtle ingress and egress features in photometric transit light curves, we investigate the effect of oblateness on the spectroscopic Rossiter–McLaughlin (RM) signals. We found that a giant planet, with planet-to-star radius ratio of 0.15 and Saturn-like oblateness of 0.098, can cause spectroscopic signatures with amplitudes up to 1.1 m s−1 which is detectable by high-precision spectrographs such as ESPRESSO. We also found that the spectroscopic oblateness signals are particularly amplified for transits across rapidly rotating stars and for planets with spin-orbit misalignment thereby making them more prominent than the photometric signals at some transit orientations. We compared the detectability of oblateness in photometry and spectroscopy and found that photometric light curves are more sensitive to detecting oblateness than the spectroscopic RM signals mostly because they can be sampled with higher cadence to better probe the oblateness ingress and egress anomaly. However, joint analyses of the light curve and RM signal of a transiting planet provides more accurate and precise estimate of the planet’s oblateness. Therefore, ESPRESSO alongside ongoing and upcoming photometric instruments such as TESS, CHEOPS, PLATO, and JWST will be extremely useful in measuring planet oblateness.
Computational tools for the spectroscopic analysis of white dwarfs
Authors: Chandra Vedant , Hwang Hsiang-Chih , Zakamska Nadia L , Budavári Tamás
Published: July 2020

The spectroscopic features of white dwarfs are formed in the thin upper layer of their stellar photosphere. These features carry information about the white dwarf’s surface temperature, surface gravity, and chemical composition (hereafter ‘labels’). Existing methods to determine these labels rely on complex ab-initio theoretical models, which are not always publicly available. Here, we present two techniques to determine atmospheric labels from white dwarf spectra: a generative fitting pipeline that interpolates theoretical spectra with artificial neural networks and a random forest regression model using parameters derived from absorption line features. We test and compare our methods using a large catalogue of white dwarfs from the Sloan Digital Sky Survey (SDSS), achieving the same accuracy and negligible bias as compared to previous studies. We package our techniques into an open-source python module ‘wdtools’ that provides a computationally inexpensive way to determine stellar labels from white dwarf spectra observed from any facility. We will actively develop and update our tool as more theoretical models become publicly available. We discuss applications of our tool in its present form to identify interesting outlier white dwarf systems including those with magnetic fields, helium-rich atmospheres, and double-degenerate binaries.
What drives galaxy quenching? Resolving molecular gas and star formation in the green valley
Authors: Brownson Simcha , Belfiore Francesco , Maiolino Roberto , Lin Lihwai , Carniani Stefano
Published: July 2020

We study quenching in seven green valley galaxies on kpc scales by resolving their molecular gas content using 12CO(1–0) observations obtained with NOrthern Extended Millimeter Array and Atacama Large Millimeter Array, and their star formation rate using spatially resolved optical spectroscopy from the Mapping Nearby Galaxies at Apache Point Observatory survey. We perform radial stacking of both data sets to increase the sensitivity to molecular gas and star formation, thereby avoiding biases against strongly quenched regions. We find that both spatially resolved gas fraction (fgas) and star formation efficiency ($\rm {SFE}$) are responsible for quenching green valley galaxies at all radii: both quantities are suppressed with respect to typical star-forming regions. fgas and $\rm {SFE}$ have roughly equal influence in quenching the outer disc. We are, however, unable to identify the dominant mechanism in the strongly quenched central regions. We find that fgas is reduced by $\rm \sim\! 1~dex$ in the central regions, but the star formation rate is too low to be measured, leading to upper limits for the $\rm {SFE}$. Moving from the outer disc to central regions, the reduction in fgas is driven by an increasing $\rm \Sigma _{\star }$ profile rather than a decreasing $\rm \Sigma _{H_{2}}$ profile. The reduced fgas may therefore be caused by a decrease in the gas supply rather than molecular gas ejection mechanisms, such as winds driven by active galactic nuclei. We warn more generally that studies investigating fgas may be deceiving in inferring the cause of quenching, particularly in the central (bulge-dominated) regions of galaxies.
Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa
Authors: Aswad Amr , Aimola Giulia , Wight Darren , Roychoudhury Pavitra , Zimmermann Cosima , Hill Joshua , Lassner Dirk , Xie Hong , Huang Meei-Li , Parrish Nicholas F , Schultheiss Heinz-Peter , Venturini Cristina , Lager Susanne , Smith Gordon C S , Charnock-Jones D Stephen , Breuer Judith , Greninger Alexander L , Kaufer Benedikt B
Published: July 2020

Human herpesvirus 6A and 6B (HHV-6) can integrate into the germline, and as a result, ∼70 million people harbor the genome of one of these viruses in every cell of their body. Until now, it has been largely unknown if 1) these integrations are ancient, 2) if they still occur, and 3) whether circulating virus strains differ from integrated ones. Here, we used next-generation sequencing and mining of public human genome data sets to generate the largest and most diverse collection of circulating and integrated HHV-6 genomes studied to date. In genomes of geographically dispersed, only distantly related people, we identified clades of integrated viruses that originated from a single ancestral event, confirming this with fluorescent in situ hybridization to directly observe the integration locus. In contrast to HHV-6B, circulating and integrated HHV-6A sequences form distinct clades, arguing against ongoing integration of circulating HHV-6A or “reactivation” of integrated HHV-6A. Taken together, our study provides the first comprehensive picture of the evolution of HHV-6, and reveals that integration of heritable HHV-6 has occurred since the time of, if not before, human migrations out of Africa.
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Authors: Shaffer Michael , Borton Mikayla A , McGivern Bridget B , Zayed Ahmed A , La Rosa Sabina Leanti , Solden Lindsey M , Liu Pengfei , Narrowe Adrienne B , Rodríguez-Ramos Josué , Bolduc Benjamin , Gazitúa M Consuelo , Daly Rebecca A , Smith Garrett J , Vik Dean R , Pope Phil B , Sullivan Matthew B , Roux Simon , Wrighton Kelly C
Published: July 2020

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout
Authors: Dantas Machado Ana Carolina , Cooper Brendon H , Lei Xiao , Di Felice Rosa , Chen Lin , Rohs Remo
Published: July 2020

Myocyte enhancer factor-2B (MEF2B) has the unique capability of binding to its DNA target sites with a degenerate motif, while still functioning as a gene-specific transcriptional regulator. Identifying its DNA targets is crucial given regulatory roles exerted by members of the MEF2 family and MEF2B’s involvement in B-cell lymphoma. Analyzing structural data and SELEX-seq experimental results, we deduced the DNA sequence and shape determinants of MEF2B target sites on a high-throughput basis in vitro for wild-type and mutant proteins. Quantitative modeling of MEF2B binding affinities and computational simulations exposed the DNA readout mechanisms of MEF2B. The resulting binding signature of MEF2B revealed distinct intricacies of DNA recognition compared to other transcription factors. MEF2B uses base readout at its half-sites combined with shape readout at the center of its degenerate motif, where A-tract polarity dictates nuances of binding. The predominant role of shape readout at the center of the core motif, with most contacts formed in the minor groove, differs from previously observed protein–DNA readout modes. MEF2B, therefore, represents a unique protein for studies of the role of DNA shape in achieving binding specificity. MEF2B–DNA recognition mechanisms are likely representative for other members of the MEF2 family.