bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)
Authors: Shao Feng , Ludwig Arne , Mao Yang , Liu Ni , Peng Zuogang
Published: August 2020

Background

The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it.

Results

The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated.

Conclusions

The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.
Broad-band ground-motion simulation of 2016 Amatrice earthquake, Central Italy
Authors: Pischiutta Marta , Akinci Aybige , Tinti Elisa , Herrero André
Published: August 2020

On 24 August 2016 at 01:36 UTC a ML6.0 earthquake struck several villages in central Italy, among which Accumoli, Amatrice and Arquata del Tronto. The earthquake was recorded by about 350 seismic stations, causing 299 fatalities and damage with macroseismic intensities up to 11. The maximum acceleration was observed at Amatrice station (AMT) reaching 916 cm s–2 on E–W component, with epicentral distance of 15 km and Joyner and Boore distance to the fault surface (RJB) of less than a kilometre. Motivated by the high levels of observed ground motion and damage, we generate broad-band seismograms for engineering purposes by adopting a hybrid method. To infer the low frequency seismograms, we considered the kinematic slip model by Tinti et al . The high frequency seismograms were produced using a stochastic finite-fault model approach based on dynamic corner-frequency. Broad-band synthetic time-series were therefore obtained by merging the low and high frequency seismograms. Simulated hybrid ground motions were compared both with the observed ground motions and the ground-motion prediction equations (GMPEs), to explore their performance and to retrieve the region-specific parameters endorsed for the simulations. In the near-fault area we observed that hybrid simulations have a higher capability to detect near source effects and to reproduce the source complexity than the use of GMPEs. Indeed, the general good consistency found between synthetic and observed ground motion (both in the time and frequency domain), suggests that the use of regional-specific source scaling and attenuation parameters together with the source complexity in hybrid simulations improves ground motion estimations. To include the site effect in stochastic simulations at selected stations, we tested the use of amplification curves derived from HVRSs (horizontal-to-vertical response spectra) and from HVSRs (horizontal-to-vertical spectral ratios) rather than the use of generic curves according to NTC18 Italian seismic design code. We generally found a further reduction of residuals between observed and simulated both in terms of time histories and spectra.
An autonomous petrological database for geodynamic simulations of magmatic systems
Authors: Rummel Lisa , Baumann Tobias S , Kaus Boris J P
Published: August 2020

Self-consistent modelling of magmatic systems is challenging as the melt continuously changes its chemical composition upon crystallization, which may affect the mechanical behaviour of the system. Melt extraction and subsequent crystallization create new rocks while depleting the source region. As the chemistry of the source rocks changes locally due to melt extraction, new calculations of the stable phase assemblages are required to track the rock evolution and the accompanied change in density. As a consequence, a large number of isochemical sections of stable phase assemblages are required to study the evolution of magmatic systems in detail. As the state-of-the-art melting diagrams may depend on nine oxides as well as pressure and temperature, this is a 10-D computational problem. Since computing a single isochemical section (as a function of pressure and temperature) may take several hours, computing new sections of stable phase assemblages during an ongoing geodynamic simulation is currently computationally intractable. One strategy to avoid this problem is to pre-compute these stable phase assemblages and to create a comprehensive database as a hyperdimensional phase diagram, which contains all bulk compositions that may emerge during petro-thermomechanical simulations. Establishing such a database would require repeating geodynamic simulations many times while collecting all requested compositions that may occur during a typical simulation and continuously updating the database until no additional compositions are required. Here, we describe an alternative method that is better suited for implementation on large-scale parallel computers. Our method uses the entries of an existing preliminary database to estimate future required chemical compositions. Bulk compositions are determined within boundaries that are defined manually or through principal component analysis in a parameter space consisting of clustered database entries. We have implemented both methods within a massively parallel computational framework while utilizing the Gibbs free energy minimization program Perple_X. Results show that our autonomous approach increases the resolution of the thermodynamic database in compositional regions that are most likely required for geodynamic models of magmatic systems.
When Ambiguous Loss Becomes Ambiguous Grief: Clinical Work with Bereaved Dementia Caregivers
Authors: Nathanson Abigail , Rogers Madeline
Published: August 2020

The experience of caring for someone with dementia can be heartbreaking. The losses inherent to caregiving itself can be difficult to reconcile after the death of a person with dementia, causing challenges in the bereavement stage. Although there is often significant social support to help people process the death of someone close to them, clinicians can struggle to help bereaved dementia caregivers integrate their ambiguous losses from caregiving, such as loss of roles, functions, and relationships, into a postdeath bereavement process. Many socioeconomic, personality, and family functioning factors impact an individual caregiver’s experience, and there are more global influences from the nature of dementia caregiving itself that must be understood to best support a caregiver. Using the lens of the dementia grief model and examples from a case study, this article seeks to illustrate the dynamics inherent in integrating ambiguous losses following the death of a person from dementia, and it proposes clinical goals for working effectively with this population.
Are Seroprevalence Estimates for Severe Acute Respiratory Syndrome Coronavirus 2 Biased?
Authors: Takahashi Saki , Greenhouse Bryan , Rodríguez-Barraquer Isabel
Published: August 2020

Biased seroprevalence estimates can occur using serological assays optimized with validation sets unrepresentative of disease spectrum in the general population. Correct interpretation of serosurveys for severe acute respiratory syndrome coronavirus 2 requires quantifying variations in sensitivity with disease severity and over time.
Eravacycline, a novel tetracycline derivative, does not induceClostridioides difficileinfection in anin vitrohuman gut model
Authors: Buckley Anthony M , Altringham James , Clark Emma , Bently Karen , Spittal William , Ewin Duncan , Wilkinson Vikki , Davis Georgina , Moura Ines B , Wilcox Mark H
Published: August 2020

Objectives

The approval of new antibiotics is essential to combat infections caused by antimicrobial-resistant pathogens; however, such agents should be tested to determine their effect on the resident microbiota and propensity to select for opportunistic pathogens, such as Clostridioides difficile. Eravacycline is a new antibiotic for the treatment of complicated intra-abdominal infections. Here, we determined the effects of eravacycline compared with moxifloxacin on the microbiota and if these were conducive to induction of C. difficile infection (CDI).

Methods

We seeded in vitro chemostat models, which simulate the physiological conditions of the human colon, with a human faecal slurry and instilled gut-reflective concentrations of either eravacycline or moxifloxacin.

Results

Eravacycline instillation was associated with decreased Bifidobacterium, Lactobacillus and Clostridium species, which recovered 1 week after exposure. However, Bacteroides spp. levels decreased to below the limit of detection and did not recover prior to the end of the experiment. Post-eravacycline, a bloom of aerobic bacterial species occurred, including Enterobacteriaceae, compared with pre-antibiotic, which remained high for the duration of the experiment. These changes in microbiota were not associated with induction of CDI, as we observed a lack of C. difficile spore germination and thus no toxin was detected. Moxifloxacin exposure sufficiently disrupted the microbiota to induce simulated CDI, where C. difficile spore germination, outgrowth and toxin production were seen.

Conclusions

These model data suggest that, despite the initial impact of eravacycline on the intestinal microbiota, similar to clinical trial data, this novel tetracycline has a low propensity to induce CDI.
What guidance does HIPAA offer to providers considering familial risk notification and cascade genetic testing?
Authors: Henrikson Nora B , Wagner Jennifer K , Hampel Heather , DeVore Christopher , Shridhar Nirupama , Williams Janet L , Donohue Katherine E , Kullo Iftikhar , Prince Anya E R
Published: August 2020

Background

It is unclear how the Health Insurance Portability and Accountability Act (HIPAA) should be interpreted in the context of sharing of genomic information between family members.

Methods

The authors analyzed the HIPAA Privacy Rule, reviewed the literature and constructed a clinical scenario to inform how HIPAA can be interpreted for multiple forms of patient- and provider-mediated genetic risk notification.

Results

Under HIPAA, healthcare providers can lawfully notify relatives to recommend genetic risk assessment using multiple approaches, including supporting the patient telling their own relatives, contacting relatives directly with the patient’s authorization, or contacting a relative’s provider directly.

Conclusions

Multiple forms of patient- or provider-mediated contact of relatives are already legally permissible under HIPAA, are consistent with ethical obligations of care to patients and their families, and could result in improved population health through identification of clinically actionable disease risk. Unanswered questions remain about implementation and impacts of provider-mediated programs.
Increased expression of the MALE STERILITY1 transcription factor gene results in temperature-sensitive male sterility in barley
Authors: Fernández-Gómez José , Talle Behzad , Wilson Zoe A
Published: August 2020

Understanding the control of fertility is critical for crop yield and breeding; this is particularly important for hybrid breeding to capitalize upon the resultant hybrid vigour. Different hybrid breeding systems have been adopted; however, these are challenging and crop specific. Mutants with environmentally reversible fertility offer valuable opportunities for hybrid breeding. The barley HvMS1 gene encodes a PHD-finger transcription factor that is expressed in the anther tapetum, which is essential for pollen development and causes complete male sterility when overexpressed in barley. This male sterility is due at least in part to indehiscent anthers resulting from incomplete tapetum degeneration, failure of anther opening, and sticky pollen under normal growth conditions (15 °C). However, dehiscence and fertility are restored when plants are grown at temperatures >20 °C, or when transferred to >20 °C during flowering prior to pollen mitosis I, with transfer at later stages unable to rescue fertility in vivo. As far as we are aware, this is the first report of thermosensitive male sterility in barley. This offers opportunities to understand the impact of temperature on pollen development and potential applications for environmentally switchable hybrid breeding systems; it also provides a ‘female’ male-sterile breeding tool that does not need emasculation to facilitate backcrossing.
Torques felt by solid accreting planets
Authors: Regály Zs
Published: August 2020

The solid material of protoplanetary discs forms an asymmetric pattern around a low-mass planet ($M_\mathrm{p}\le 10\, \mathrm{ M}_\oplus$) due to the combined effect of dust–gas interaction and the gravitational attraction of the planet. Recently, it has been shown that although the total solid mass is negligible compared to that of gas in protoplanetary discs, a positive torque can be emerged by a certain size solid species. The torque magnitude can overcome that of gas which may result in outward planetary migration. In this study, we show that the accretion of solid species by the planet strengthens the magnitude of solid torque being either positive or negative. We run two-dimensional, high-resolution ($1.5\,\rm {K}\times 3\,\rm {K}$) global hydrodynamic simulations of an embedded low-mass planet in a protoplanetary disc. The solid material is handled as a pressureless fluid. Strong accretion of well-coupled solid species by an $M_\mathrm{p}\lesssim 0.3\, \mathrm{ M}_\oplus$ protoplanet results in the formation of such a strongly asymmetric solid pattern close to the planet that the positive solid torque can overcome that of gas by two times. However, the accretion of solids in the pebble regime results in increased magnitude negative torque felt by protoplanets and strengthened positive torque for Earth-mass planets. For $M_\mathrm{p}\ge 3\, \mathrm{ M}_\oplus$ planets, the magnitude of the solid torque is positive, however, independent of the accretion strength investigated. We conclude that the migration of solid accreting planets can be substantially departed from the canonical type-I prediction.
Chemical fingerprints of formation in rocky super-Earths’ data
Authors: Plotnykov Mykhaylo , Valencia Diana
Published: August 2020

The composition of rocky exoplanets in the context of stars’ composition provides important constraints to formation theories. In this study, we select a sample of exoplanets with mass and radius measurements with an uncertainty $\lt 25{{\ \rm per\ cent}}$ and obtain their interior structure. We calculate compositional markers, ratios of iron to magnesium and silicon, as well as core mass fractions (CMFs) that fit the planetary parameters, and compare them to the stars. We find four key results that successful planet formation theories need to predict: (1) In a population sense, the composition of rocky planets spans a wider range than stars. The stars’ Fe/Si distribution is close to a Gaussian distribution $1.63^{+0.91}_{-0.85}$, while the planets’ distribution peaks at lower values and has a longer tail, $1.15^{+1.43}_{-0.76}$. It is easier to see the discrepancy in CMF space, where primordial stellar composition is $0.32^{+0.14}_{-0.12}$, while rocky planets follow a broader distribution $0.24^{+0.33}_{-0.18}$. (2) We introduce uncompressed density ($\overline{\rho _0}$ at reference pressure/temperature) as a metric to compare compositions. With this, we find what seems to be the maximum iron enrichment that rocky planets attain during formation ($\overline{\rho _0}\sim 6$ and CMF ∼0.8). (3) Highly irradiated planets exhibit a large range of compositions. If these planets are the result of atmospheric evaporation, iron enrichment and perhaps depletion must happen before gas dispersal. And, (4) We identify a group of highly irradiated planets that, if rocky, would be twofold depleted in Fe/Si with respect to the stars. Without a reliable theory for forming iron-depleted planets, these are interesting targets for follow-up.
A disc reflection model for ultra-soft narrow-line Seyfert 1 galaxies
Authors: Jiang Jiachen , Gallo Luigi C , Fabian Andrew C , Parker Michael L , Reynolds Christopher S
Published: August 2020

We present a detailed analysis of the XMM–Newton observations of five narrow-line Seyfert 1 galaxies (NLS1s). They all show very soft continuum emission in the X-ray band with a photon index of Γ ≳ 2.5. Therefore, they are referred to as ‘ultra-soft’ NLS1s in this paper. By modelling their optical/UV–X-ray spectral energy distribution (SED) with a reflection-based model, we find indications that the disc surface in these ultra-soft NLS1s is in a higher ionization state than other typical Seyfert 1 AGN. Our best-fitting SED models suggest that these five ultra-soft NLS1s have an Eddington ratio of λEdd = 1–20 assuming available black hole mass measurements. In addition, our models infer that a significant fraction of the disc energy in these ultra-soft NLS1s is radiated away in the form of non-thermal emission instead of the thermal emission from the disc. Due to their extreme properties, X-ray observations of these sources in the iron band are particularly challenging. Future observations, e.g. from Athena, will enable us to have a clearer view of the spectral shape in the iron band and thus distinguish the reflection model from other interpretations of their broad-band spectra.
Radio emission from a decade old Type I superluminous supernova, PTF10hgi: comparison with FRB121102
Authors: Mondal Surajit , Bera Apurba , Chandra Poonam , Das Barnali
Published: August 2020

We perform a comparative study between the only radio-detected Type I superluminous supernova (SLSN) PTF10hgi, and the most active repeating fast radio burst FRB121102. This study has its root in the hypothesized FRB-SLSN connection that states that magnetars born in SLSN can power FRBs. The wide-band spectrum (0.6–15 GHz) of PTF10hgi presented here, provides strong evidence for the magnetar wind nebular origin of the radio emission. The same spectrum also enables us to make robust estimates of the radius and the magnetic field of the radio-emitting region and demonstrates that the nebula is powered by the rotational energy of the magnetar. This spectrum is then compared with that of FRB121102 which we extend down to 400 MHz using archival data. The newly added measurements put very tight constraint on the emission models of the compact persistent source associated with FRB121102. We find that while both sources can be powered by the rotational energy of the underlying magnetar, the average energy injection rate is much higher in FRB121102. Hence, we hypothesize that, if PTF10hgi is indeed emitting fast radio bursts, those will be much weaker energetically than those from FRB121102.
Return of the Big Glitcher: NICER timing and glitches of PSR J0537−6910
Authors: Ho Wynn C G , Espinoza Cristóbal M , Arzoumanian Zaven , Enoto Teruaki , Tamba Tsubasa , Antonopoulou Danai , Bejger Michał , Guillot Sebastien , Haskell Brynmor , Ray Paul S
Published: August 2020

PSR J0537−6910, also known as the Big Glitcher, is the most prolific glitching pulsar known, and its spin-induced pulsations are only detectable in X-ray. We present results from analysis of 2.7 yr of NICER timing observations, from 2017 August to 2020 April. We obtain a rotation phase-connected timing model for the entire time span, which overlaps with the third observing run of LIGO/Virgo, thus enabling the most sensitive gravitational wave searches of this potentially strong gravitational wave-emitting pulsar. We find that the short-term braking index between glitches decreases towards a value of 7 or lower at longer times since the preceding glitch. By combining NICER and RXTE data, we measure a long-term braking index n = −1.25 ± 0.01. Our analysis reveals eight new glitches, the first detected since 2011, near the end of RXTE, with a total NICER and RXTE glitch activity of $8.88\times 10^{-7}\, \mathrm{yr^{-1}}$. The new glitches follow the seemingly unique time-to-next-glitch–glitch-size correlation established previously using RXTE data, with a slope of $5\, \rm {d} \, \mu \mathrm{Hz}^{-1}$. For one glitch around which NICER observes 2 d on either side, we search for but do not see clear evidence of spectral nor pulse profile changes that may be associated with the glitch.
Concordance cosmology?
Authors: Park Youngsoo , Rozo Eduardo
Published: August 2020

We propose a new intuitive metric for evaluating the tension between two experiments, and apply it to several data sets. While our metric is non-optimal, if evidence of tension is detected, this evidence is robust and easy to interpret. Assuming a flat Lambda cold dark matter (ΛCDM) cosmological model, we find that there is a modest 2.2σ tension between the Dark Energy Survey (DES) Year 1 results and the Planck measurements of the cosmic microwave background. This tension is driven by the difference between the amount of structure observed in the late-time Universe and that predicted from fitting the Planck data, and appears to be unrelated to the tension between Planck and local estimates of the Hubble rate. In particular, combining DES, baryon acoustic oscillations, big bang nucleosynthesis, and supernovae measurements recover a Hubble constant and sound horizon consistent with Planck, and in tension with local distance–ladder measurements. If the tension between these various data sets persists, it is likely that reconciling all current data will require breaking the flat ΛCDM model in at least two different ways: one involving new physics in the early Universe, and one involving new late-time Universe physics.
Seropositive PLA2R-associated membranous nephropathy but biopsy-negative PLA2R staining
Authors: Luo Jiao , Zhang Wang , Su Cailing , Zhou Zhanmei , Wang Guobao
Published: August 2020

Background

Serum phospholipase A2 receptor (PLA2R) antibody (SAb) and glomerular deposits of PLA2R antigen (GAg) have been tested widely in idiopathic membranous nephropathy (MN). Recently, we noticed a special form of PLA2R-associated MN with positive circulating PLA2R antibody but negative PLA2R deposits in the glomeruli by immunofluorescence on frozen tissue (IF-F). The significance of this form of PLA2R-associated MN is yet to be elucidated. This study aimed to explore the clinicopathological features of these PLA2R-associated MN patients.

Methods

This study enrolled 229 biopsy-proven PLA2R-associated MN patients with SAb+. SAb was measured by enzyme-linked immunosorbent assay, and GAg was detected by IF-F. These patients were divided into SAb+/GAg+ and SAb+/GAg− groups. Clinicopathological characteristics of SAb+/GAg+ and SAb+/GAg− PLA2R-associated MN patients were compared. PLA2R antigens of 19 SAb+/GAg− PLA2R-associated MN patients were verified by immunohistochemistry on paraffin tissue (IHC-P).

Results

Among 229 SAb+ PLA2R-associated MN patients, 210 (91.70%) were GAg+ and 19 (8.3%) were GAg−. These 19 SAb+/GAg− PLA2R-associated MN patients presented positive PLA2R deposits by IHC-P. Compared with SAb+/GAg+ PLA2R-associated MN patients, SAb+/GAg- PLA2R-associated MN patients had higher levels of serum PLA2R antibody (P = 0.004), increased proteinuria (P = 0.008), lower serum albumin (P = 0.019), more prominent chronic pathological lesions in terms of glomerulosclerosis score (P = 0.025), interstitial fibrosis score (P = 0.016), tubular atrophy score (P = 0.010) and total renal chronicity score (P = 0.010), and were more likely to be accompanied by focal segmental glomerulosclerosis (P = 0.014). Higher SAb level was associated with the total renal chronicity score (odds ratio per 100 RU/mL, 1.16; 95% confidence interval 1.01–1.33; P = 0.033).

Conclusions

PLA2R-associated MN patients with seropositive PLA2R antibody but negative PLA2R deposits in the glomeruli by IF-F have higher levels of SAb and worse clinicopathological manifestations compared with their double-positive counterparts. IHC-P can be an alternative technique to reveal PLA2R glomerular deposits.
The natural compound obtusaquinone targets pediatric high-grade gliomas through ROS-mediated ER stress
Authors: Teng Jian , Lashgari Ghazal , Tabet Elie I , Tannous Bakhos A
Published: August 2020

Background

Pediatric high-grade gliomas (pHGGs) are aggressive primary brain tumors with local invasive growth and poor clinical prognosis. Treatment of pHGGs is particularly challenging given the intrinsic resistance to chemotherapy, an absence of novel therapeutics, and the difficulty of drugs to reach the tumor beds. Accumulating evidence suggests that production of reactive oxygen species (ROS) and misfolded proteins, which typically leads to endoplasmic reticulum (ER) stress, is an essential mechanism in cancer cell survival.

Methods

Several cell viability assays were used in 6 patient-derived pHGG cultures to evaluate the effect of the natural compound obtusaquinone (OBT) on cytotoxicity. Orthotopic mouse models were used to determine OBT effects in vivo. Immunoblotting, immunostaining, flow cytometry, and biochemical assays were used to investigate the OBT mechanism of action.

Results

OBT significantly inhibited cell survival of patient-derived pHGG cells in culture. OBT inhibited tumor growth and extended survival in 2 different orthotopic xenograft models. Mechanistically, OBT induced ER stress through abnormal ROS accumulation.

Conclusion

Our data demonstrate the utility and feasibility of OBT as a potential therapeutic option for improving the clinical treatment of pHGGs.
Development of a space cold atom clock
Authors: Ren Wei , Li Tang , Qu Qiuzhi , Wang Bin , Li Lin , Lü Desheng , Chen Weibiao , Liu Liang
Published: August 2020

Atomic clocks with cold atoms play important roles in the field of fundamental physics as well as primary frequency standards. Operating such cold atom clocks in space paves the way for further exploration in fundamental physics, for example dark matter and general relativity. We developed a space cold atom clock (SCAC), which was launched into orbit with the Space Lab TG-2 in 2016. Before it deorbited with TG-2 in 2019, the SCAC had been working continuously for almost 3 years. During the period in orbit, many scientific experiments and engineering tests were performed. In this article, we summarize the principle, development and in-orbit results. These works provide the basis for construction of a space-borne time-frequency system in deep space.
Electronic structures and topological properties in nickelatesLnn+1NinO2n+2
Authors: Gao Jiacheng , Peng Shiyu , Wang Zhijun , Fang Chen , Weng Hongming
Published: August 2020

After the significant discovery of the hole-doped nickelate compound Nd0.8Sr0.2NiO2, analyses of the electronic structure, orbital components, Fermi surfaces and band topology could be helpful to understand the mechanism of its superconductivity. Based on first-principle calculations, we find that Ni $3d_{x^2-y^2}$ states contribute the largest Fermi surface. The $Ln 5d_{3z^2-r^2}$ states form an electron pocket at Γ, while 5dxy states form a relatively bigger electron pocket at A. These Fermi surfaces and symmetry characteristics can be reproduced by our two-band model, which consists of two elementary band representations: B1g@1a ⊕ A1g@1b. We find that there is a band inversion near A, giving rise to a pair of Dirac points along M-A below the Fermi level upon including spin-orbit coupling. Furthermore, we perform density functional theory based Gutzwiller (DFT+Gutzwiller) calculations to treat the strong correlation effect of Ni 3d orbitals. In particular, the bandwidth of $3d_{x^2-y^2}$ has been renormalized largely. After the renormalization of the correlated bands, the Ni 3dxy states and the Dirac points become very close to the Fermi level. Thus, a hole pocket at A could be introduced by hole doping, which may be related to the observed sign change of the Hall coefficient. By introducing an additional Ni 3dxy orbital, the hole-pocket band and the band inversion can be captured in our modified model. Besides, the nontrivial band topology in the ferromagnetic two-layer compound La3Ni2O6 is discussed and the band inversion is associated with Ni $3d_{x^2-y^2}$ and La 5dxy orbitals.
George Buchanan
Authors: Reid Steven J.
Published: August 2020

Although his name is now virtually unknown beyond academia, George Buchanan (b. 1506–d. 1582) was one of the foremost humanists and Neo-Latinists of the 16th century. His work as a writer, polemicist, and educator had a Europe-wide impact in his own lifetime, and a cultural afterlife so great that it resulted in a large obelisk being erected in his memory in his hometown of Killearn, Scotland, and year-long public celebrations of the four-hundredth anniversary of his birth at the Universities of Glasgow and St. Andrews in 1906. Buchanan is best known to early modern historians as the polemicist for the revolutionary party that forced Mary Stuart to abdicate from the throne of Scotland in 1567 in favor of her infant son, James. It was in this context that he produced a scurrilous account of her reign (the De Maria Regina Scotorum, published in English as the Detectioun), an explosive treatise on the nature of Scottish kingship and the right to resist and kill tyrants (the De Iure Regni apud Scotos Dialogus), and a history of Scotland (Rerum Scoticarum Historia) that acted as a “proof text” of sorts for his theories on monarchy. Buchanan was also tutor to Mary’s son, who as James VI and I would become arguably the most literary British monarch ever to sit on the throne. To scholars of the French Renaissance, Buchanan is more famous—and has been studied in comparatively much greater depth—as the author of Neo-Latin works across an impressive range of genres, many of which strongly influenced early French vernacular literature. These included religious tragedies and translations of ancient Greek plays (Jephthes, Baptistes, Alcestis, Medea), and secular and anti-clerical poetry (the Franciscanus, written in Scotland for James V around 1537, being the most famous example). His crowning poetic achievement, the Latin versification and paraphrasing of the complete Hebrew Psalter, was begun while he was imprisoned by the Inquisition in Portugal, where he had been one of the first teachers at the newly established University of Coimbra. Once safely back in France and then Scotland, the complete collection was published in stages, and it enjoyed exceptional critical acclaim and international dissemination. The psalm paraphrases would see Buchanan receive the epithet (at least according to his publisher) of “easily the prince of poets of our age” (poetarum nostri saeculi facile princeps). He died in 1582, but his works and ideas circulated among poets, intellectuals, and revolutionary parties alike for centuries after.
Natural Resources, Energy Politics, and Environmental Consequences
Authors: Kröger Markus
Published: August 2020

Life on Earth is undergoing major changes due to the converging and rapidly accelerating climate, biodiversity, pollution, and other environmental crises and emergencies. Global environmental and ecological constraints, consequences, and politics are becoming mainstream and necessary components to include in analysis across scientific fields. Over-extraction of resources in destructive ways is leading key ecosystems into states of collapse, species and habitats are being lost at record rates, and tipping points are cascading to produce a chaotic transformation. In this setting, resource extraction, in its varied forms, needs to be urgently analyzed in terms of its impacts and politics to understand, explain, transform, regulate, and govern the way natural resource sectors and actors affect the web of life. To this end, this article opens up natural resource politics, and how their unfolding has been analyzed globally and sectorially. Most of the studies related to or discussing the topic of extraction focus on the negative impacts of these projects, their developmental impacts, or the characteristics of conflicts related to extraction. Fewer studies focus on explaining what are the politics that lead to negative impacts, development, or conflicts. The studies on the politics behind extractive investment outcomes discuss the causal paths from political actions to extraction in different contexts mostly tangentially. Yet, constructivist studies by social scientists on natural resources have shown how resources and spaces of extracting resources are also created in social and political processes, which are typically international and related to existing power relations. Resources do not just exist out there, but are imagined when a part of nature is framed as a natural resource, and some areas are turned into sacrifice zones for extraction. These are places being destroyed as they do not matter to their extractors. The span of these localities has expanded over nations and subcontinents, placing us all in the sacrifice zone now, as Naomi Klein elucidates in This Changes Everything: Capitalism vs. the Climate. This bibliography covers first the textbooks, followed by an assessment of the key dynamics in which resource politics are embedded, such as conflicts and developmental interventions, and their key actors: civil society, corporations, states, and global actors. Last, the particularities for different targets and sectors of extraction are assessed, including trees and forests, minerals, hydrocarbons and energy, water, and food and feed. For databases and resources, journals, and methodology of studying resource politics, please see the Oxford Bibliographies article “Politics of Extraction: Theories and New Concepts for Critical Analysis” which focuses on the key theories and organizing concepts.
Archaeobotany
Authors: McClatchie Meriel
Published: August 2020

Archaeobotany explores people’s engagement with plants and landscapes through analysis of preserved plant remains. Delicate, sometimes fragmentary, remains of plants are often recovered from archaeological excavations because in certain conditions this material can survive for thousands of years. When identified, plant remains enable the archaeobotanist to reveal how humans created, modified, and engaged with their physical and social environments through space and time. A wide variety of research questions can be explored in archaeobotany, including foodways, agricultural and other management practices, environments, medicines, textiles, structures, and furnishings. In its methodological and theoretical approaches, archaeobotany draws from many disciplines, including botany, plant genetics, agricultural studies, ethnography, history, and archaeology. Terms other than archaeobotany are sometimes used to refer to this discipline, including “palaeoethnobotany” and “palaeobotany.” The term “palaeoethnobotany” emphasizes human interactions with plants, while “palaeobotany” is focused on environments. The term “archaeobotany” is more appropriate because it combines the study of both human interactions and landscapes, and this dual approach is better suited to research objectives in archaeology. There are two broad groups of material in archaeobotany: macro-remains and micro-remains. Plant macro-remains are more often studied, but analysis of micro-remains is becoming increasingly popular. Plant macro-remains usually refer to plant structures that can be seen with the naked eye (often >0.5mm) but require low-powered microscopy for identification. Seeds and fruits of higher plants are most often studied, including cereal grains and chaff, nuts and nutshell, stones and seeds of fruits, and seeds of wild plants (the word “seed” is used here in its broadest sense). Other plant macro-remains, some of which require higher-powered microscopy, can include remains of cooked food, cereal bran (part of the periderm of the grass caryopsis), vegetative components of plants (such as leaves, bud scales and thorns), parenchyma (underground storage organs of plants, such as roots and tubers), plant fibers, wood and charcoal, and lower plants, such as mosses and fungi. Commonly investigated plant micro-remains include pollen, phytoliths, and starch grains. Some categories of remains (such as seeds) can inform on local, short-term human interactions with plants, whereas others (such as pollen) can reflect regional, longer-term interactions. The category of plant remains selected for analysis will usually depend on research questions and expected preservation conditions.
Fernando de Alva Ixtlilxochitl
Authors: Brian Amber
Published: August 2020

Don Fernando de Alva Ixtlilxochitl (b. c. 1578–d. 1650) is a relatively unknown figure outside of specialist academic circles, yet he has been very influential in the development of the historiography of pre-Hispanic central Mexico, or Anahuac. Born in the last quarter of the 16th century, his family had roots in Anahuac and in Spain. His mother was descended from elite native rulers of the city of Tetzcoco, while his father was a Spanish settler who worked as a Nahuatl-Spanish interpreter in the courts of Mexico City. Alva Ixtlilxochitl also served as an interpreter and as a bureaucratic official in the colonial government. During his lifetime, Alva Ixtlilxochitl’s family’s wealth and status were tied to his mother’s and grandmother’s connections to the family’s cacicazgo (landed estate) in San Juan Teotihuacan. Yet it was his ancestors from Tetzcoco who were the primary object of study in his five historical works. In four historical accounts and his magnum opus, the History of the Chichimeca Nation (2019, cited under Manuscripts, Editions, Translations), Alva Ixtlilxochitl recounts the origins, deeds, and exploits of the leaders of Tetzcoco, including the renowned Nezahualcoyotl (r. 1429–1472) and Nezahualpilli (r. 1472–1515). For these histories he relied on native sources. As he says himself in the prefatory materials to the History of the Chichimeca Nation, these sources included “painted histories and annals and the songs with which they preserved them,” and to make sense of these materials he sought out “the elders of New Spain who were renowned for their knowledge and understanding of those stories” (History of the Chichimeca Nation, p. 29). The result of Alva Ixtlilxochitl’s research and writing has left an important legacy in studies of the history of ancient Mexico. Scholars from the 17th century onward drew on Alva Ixtlilxochitl’s representations of pre-Hispanic and conquest-era Mexico to such an extent that his depictions of Tetzcoco as a center of learning and culture and his depictions of Nezahualcoyotl as a revered poet-king became standard in both academic studies and popular culture. Burgeoning scholarly interest in mestizo historians in the 1990s brought renewed attention to Alva Ixtlilxochitl’s writings and to his position as a colonial subject and author, while the rediscovery of Alva Ixtlilxochitl’s original manuscripts in the 1980s provided new material sources with which to study the creation and impact of his works. Alva Ixtlilxochitl’s own projects and his legacy represent an important reminder of how, on occasion, the stories and storytelling of native peoples survived the brutalities of conquest and colonialism.
Lee Chang-dong
Authors: Raymond Marc
Published: August 2020

Lee Chang-dong, born in 1954 in Daegu, South Korea, came to the cinema after a career writing fiction, wanting to reach a large audience with his work, and believing this was no longer possible using the written word. He began by working on two scripts for Korean New Wave director Park Kwang-su: Geu seome gago shibda (To the Starry Island) (1993) and Jeon Tae-il (A Single Spark) (1995). Soon, he would go on to make his first film as a writer-director, Chorok Mulgogi (Green Fish) (1997), part of a whole cohort of filmmakers (Hong Sang-soo, Kim Ki-duk, Park Chan-wook, Bong Joon-ho) who would remake the Korean film industry over the upcoming decades. Lee’s work is both distinctive among his Korean contemporaries, tending more toward realism in style even as he deals with the melodramatic plots required of mainstream cinema, while being more continuous with Western art cinema humanism than cultish genre directors like Park and Bong or more minimalist stylists like Hong. His next film, Bakha Satang (Peppermint Candy) (1999), would establish Lee as an important voice, and although he would work slowly over the next coming decades, each new Lee film would mark an important event both in Korean cinema and, increasingly, in the global market as well. It was also at this time that Western scholarly interest in Korean film begins to widely expand, and Lee’s movies were often an important touchstone for this work. In 2002, he released Oasis (2002), which competed at the Venice Film Festival, and then he made another change in his career direction, becoming the minister of culture and tourism under the left-wing government of Roh Moo-hyun from 2003 to 2004. He returned to filmmaking in 2007 with his first literary adaptation, Milyang (Secret Sunshine), which won a Best Actress award for Jeon Do-yeon at the Cannes Film Festival. His next film, Shi (Poetry), was almost universally acclaimed and won the Best Screenplay award at Cannes, but then Lee took another sustained break from directing, although he did help produce some important films, such as July Jang’s Dohee-ya (A Girl at My Door) (2012) and Yoon Ga-eun’s Woori-deul (The World of Us) (2016). In 2018, he returned with his most unusual film to date, Burning, a (relatively) big-budget adaptation of a short story by Haruki Murakami. It won the International Critics Prize at Cannes and reestablished Lee as one of the modern cinema’s master filmmakers. In 2022, his short film Shin-jang-so-ri (Heartbeat) premiered at the Jeonju International Film Festival along with a remastered retrospective of his six features and an accompanying collection of essays, published simultaneously in Korean and English translations.
Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya
Authors: Luka Martha M , Kamau Everlyn , Adema Irene , Munywoki Patrick K , Otieno Grieven P , Gicheru Elijah , Gichuki Alex , Kibinge Nelson , Agoti Charles N , Nokes D James
Published: August 2020

Background

Human rhinovirus (HRV) is the most common cause of the common cold but may also lead to more severe respiratory illness in vulnerable populations. The epidemiology and genetic diversity of HRV within a school setting have not been previously described. The objective of this study was to characterize HRV molecular epidemiology in a primary school in a rural location of Kenya.

Methods

Between May 2017 and April 2018, over 3 school terms, we collected 1859 nasopharyngeal swabs (NPS) from pupils and teachers with symptoms of acute respiratory infection in a public primary school in Kilifi County, coastal Kenya. The samples were tested for HRV using real-time reverse transcription polymerase chain reaction. HRV-positive samples were sequenced in the VP4/VP2 coding region for species and genotype classification.

Results

A total of 307 NPS (16.4%) from 164 individuals were HRV positive, and 253 (82.4%) were successfully sequenced. The proportion of HRV in the lower primary classes was higher (19.8%) than upper primary classes (12.2%; P < .001). HRV-A was the most common species (134/253; 53.0%), followed by HRV-C (73/253; 28.9%) and HRV-B (46/253; 18.2%). Phylogenetic analysis identified 47 HRV genotypes. The most common genotypes were A2 and B70. Numerous (up to 22 in 1 school term) genotypes circulated simultaneously, there was no individual re-infection with the same genotype, and no genotype was detected in all 3 school terms.

Conclusions

HRV was frequently detected among school-going children with mild acute respiratory illness symptoms, particularly in the younger age groups (<5-year-olds). Multiple HRV introductions were observed that were characterized by considerable genotype diversity.
The Antibody Response to SARS-CoV-2 Infection
Authors: Hueston Linda , Kok Jen , Guibone Ayla , McDonald Damien , Hone George , Goodwin James , Carter Ian , Basile Kerri , Sandaradura Indy , Maddocks Susan , Sintchenko Vitali , Gilroy Nicole , Chen Sharon , Dwyer Dominic E , O’Sullivan Matthew V N
Published: August 2020

Background

Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–specific antibodies has become an important tool, complementing nucleic acid tests (NATs) for diagnosis and for determining the prevalence of coronavirus disease 2019 (COVID-19) in population serosurveys. The magnitude and persistence of antibody responses are critical for assessing the duration of immunity.

Methods

A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for immunoglobulin G (IgG), immunoglobulin A (IgA), and immunoglobulin M (IgM) was developed and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Neutralizing antibody responses were measured in a subset of samples using a standard microneutralization assay.

Results

A total of 2753 individuals were eligible for the study (126 NAT-positive; prevalence, 4.6%). The median “window period” from illness onset to appearance of antibodies (range) was 10.2 (5.8–14.4) days. The sensitivity and specificity of either SARS-CoV-2 IgG, IgA, or IgM when collected ≥14 days after symptom onset were 91.3% (95% CI, 84.9%–95.6%) and 98.9% (95% CI, 98.4%–99.3%), respectively. The negative predictive value was 99.6% (95% CI, 99.3%–99.8%). The positive predictive value of detecting any antibody class was 79.9% (95% CI, 73.3%–85.1%); this increased to 96.8% (95% CI, 90.7%–99.0%) for the combination of IgG and IgA.

Conclusions

Measurement of SARS-CoV-2-specific antibody by IFA is an accurate method to diagnose COVID-19. Serological testing should be incorporated into diagnostic algorithms for SARS-CoV-2 infection to identify additional cases where NAT was not performed and resolve cases where false-negative and false-positive NATs are suspected. The majority of individuals develop robust antibody responses following infection, but the duration of these responses and implications for immunity remain to be established.