bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of spironolactone on cardiovascular function and markers of fibrosis in people at increased risk of developing heart failure: the heart ‘OMics’ in AGEing (HOMAGE) randomized clinical trial
Authors: Cleland John G F , Ferreira João Pedro , Mariottoni Beatrice , Pellicori Pierpaolo , Cuthbert Joe , Verdonschot Job A J , Petutschnigg Johannes , Ahmed Fozia Z , Cosmi Franco , Brunner La Rocca Hans-Peter , Mamas Mamas A , Clark Andrew L , Edelmann Frank , Pieske Burkert , Khan Javed , McDonald Ken , Rouet Philippe , Staessen Jan A , Mujaj Blerim , González Arantxa , Diez Javier , Hazebroek Mark , Heymans Stephane , Latini Roberto , Grojean Stéphanie , Pizard Anne , Girerd Nicolas , Rossignol Patrick , Collier Tim J , Zannad Faiez ,   the HOMAGE Trial Committees and Investigators, Atar Dan , Kober Lars , Dickstein Kenneth , Lange Theis
Published: September 2020

Aims 

To investigate the effects of spironolactone on fibrosis and cardiac function in people at increased risk of developing heart failure.

Methods and results 

Randomized, open-label, blinded-endpoint trial comparing spironolactone (50 mg/day) or control for up to 9 months in people with, or at high risk of, coronary disease and raised plasma B-type natriuretic peptides. The primary endpoint was the interaction between baseline serum galectin-3 and changes in serum procollagen type-III N-terminal pro-peptide (PIIINP) in participants assigned to spironolactone or control. Procollagen type-I C-terminal pro-peptide (PICP) and collagen type-1 C-terminal telopeptide (CITP), reflecting synthesis and degradation of type-I collagen, were also measured. In 527 participants (median age 73 years, 26% women), changes in PIIINP were similar for spironolactone and control [mean difference (mdiff): −0.15; 95% confidence interval (CI) −0.44 to 0.15 μg/L; P = 0.32] but those receiving spironolactone had greater reductions in PICP (mdiff: −8.1; 95% CI −11.9 to −4.3 μg/L; P < 0.0001) and PICP/CITP ratio (mdiff: −2.9; 95% CI −4.3 to −1.5; <0.0001). No interactions with serum galectin were observed. Systolic blood pressure (mdiff: −10; 95% CI −13 to −7 mmHg; P < 0.0001), left atrial volume (mdiff: −1; 95% CI −2 to 0 mL/m2; P = 0.010), and NT-proBNP (mdiff: −57; 95% CI −81 to −33 ng/L; P < 0.0001) were reduced in those assigned spironolactone.

Conclusions 

Galectin-3 did not identify greater reductions in serum concentrations of collagen biomarkers in response to spironolactone. However, spironolactone may influence type-I collagen metabolism. Whether spironolactone can delay or prevent progression to symptomatic heart failure should be investigated.
Associations between BMI and visual impairment of 33 407 preschool children in Germany: a pooled cross-sectional study
Authors: Liu Weina , Schwertz Rainer , Welker Andreas , Welker Judith , Chen Simiao , Dambach Peter , Marx Michael
Published: September 2020

Background

Prevalence of overweight and obesity in Germany is increasing. High body weight can affect children’s growth and development. This paper aimed to determine the association between body mass index (BMI) and visual impairment among preschool children and explore the potential role of obesity in predicting visual developmental disorder.

Methods

Six consecutive years of data from the School Entry Examination were collected for all preschool children aged from 4 to 6 years residing in Rhine-Neckar County and the City of Heidelberg, Germany from 2013 to 2018. Univariate and multivariate regression were used to analyze the complete data, multiple imputation was used to deal with missing data.

Results

Among the group with an immigrant background, children with obesity [OR = 1.20, 99% (1.02–1.42)] were more likely to have visual impairment compared to those with normal body weight (P < 0.01) after adjusting for survey year, age, and gender of children, education and occupation of parents, screen time-frequency, whether a television was in their bedroom, and quality of preschool outdoor environment.

Conclusion

There were significant associations between obesity and visual impairment among German preschool children with immigrant backgrounds. Strategies to support vulnerable groups were needed across all regional schools.
Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi
Authors: Pizarro David , Divakar Pradeep K , Grewe Felix , Crespo Ana , Dal Grande Francesco , Lumbsch Helge Thorsten
Published: September 2020

Lichen-forming fungi are known to produce a large number of secondary metabolites. Some metabolites are deposited in the cortical layer of the lichen thallus where they exert important ecological functions, such as UV filtering. The fact that closely related lineages of lichen-forming fungi can differ in cortical chemistry suggests that natural product biosynthesis in lichens can evolve independent from phylogenetic constraints. Usnic acid is one of the major cortical pigments in lichens. Here we used a comparative genomic approach on 46 lichen-forming fungal species of the Lecanoromycetes to elucidate the biosynthetic gene content and evolution of the gene cluster putatively responsible for the biosynthesis of usnic acid. Whole-genome sequences were gathered from taxa belonging to different orders and families of Lecanoromycetes, where Parmeliaceae is the most well-represented taxon, and analyzed with a variety of genomic tools. The highest number of biosynthetic gene clusters was found in Evernia prunastri, Pannoparmelia angustata, and Parmotrema austrosinense, respectively, and lowest in Canoparmelia nairobiensis, Bulbothrix sensibilis, and Hypotrachyna scytodes. We found that all studied species producing usnic acid contain the putative usnic acid biosynthetic gene cluster, whereas the cluster was absent in all genomes of species lacking usnic acid. The absence of the gene cluster was supported by an additional unsuccessful search for ß-ketoacylsynthase, the most conserved domain of the gene cluster, in the genomes of species lacking usnic acid. The domain architecture of this PKS cluster—homologous to the already known usnic acid PKS cluster (MPAS) and CYT450 (MPAO)—varies within the studied species, whereas the gene arrangement is highly similar in closely related taxa. We hypothesize that the ancestor of these lichen-forming fungi contained the putative usnic acid producing PKS cluster and that the gene cluster was lost repeatedly during the evolution of these groups. Our study provides insight into the genomic adaptations to the evolutionary success of these lichen-forming fungal species and sets a baseline for further exploration of biosynthetic gene content and its evolutionary significance.
What Determines Cognitive Functioning in the Oldest-Old? The EMIF-AD 90+ Study
Authors: Legdeur Nienke , Badissi Maryam , Yaqub Maqsood , Beker Nina , Sudre Carole H , ten Kate Mara , Gordon Mark Forrest , Novak Gerald , Barkhof Frederik , van Berckel Bart N M , Holstege Henne , Muller Majon , Scheltens Philip , Maier Andrea B , Visser Pieter Jelle
Published: September 2020

Objectives

Determinants of cognitive functioning in individuals aged 90 years and older, the oldest-old, remain poorly understood. We aimed to establish the association of risk factors, white matter hyperintensities (WMHs), hippocampal atrophy, and amyloid aggregation with cognition in the oldest-old.

Method

We included 84 individuals without cognitive impairment and 38 individuals with cognitive impairment from the EMIF-AD 90+ Study (mean age 92.4 years) and tested cross-sectional associations between risk factors (cognitive activity, physical parameters, nutritional status, inflammatory markers, and cardiovascular risk factors), brain pathology biomarkers (WMH and hippocampal volume on magnetic resonance imaging, and amyloid binding measured with positron emission tomography), and cognition. Additionally, we tested whether the brain pathology biomarkers were independently associated with cognition. When applicable, we tested whether the effect of risk factors on cognition was mediated by brain pathology.

Results

Lower values for handgrip strength, Short Physical Performance Battery (SPPB), nutritional status, HbA1c, and hippocampal volume, and higher values for WMH volume and amyloid binding were associated with worse cognition. Higher past cognitive activity and lower body mass index were associated with increased amyloid binding, lower muscle mass with more WMH, and lower SPPB scores with more WMH and hippocampal atrophy. The brain pathology markers were independently associated with cognition. The association of SPPB with cognition was partially mediated by hippocampal volume.

Discussion

In the oldest-old, physical parameters, nutritional status, HbA1c, WMH, hippocampal atrophy, and amyloid binding are associated with cognitive impairment. Physical performance may affect cognition through hippocampal atrophy. This study highlights the importance to consider multiple factors when assessing cognition in the oldest-old.
Age-Related Attributions of Experienced Changes in Life: Origins and Implications
Authors: Rothermund Klaus , de Paula Couto Maria Clara Pinheiro , Fung Helene H , Graf Sylvie , Hess Thomas M , Liou Shyhnan , Nikitin Jana
Published: September 2020

Objectives

Attributing life changes to age represents a core marker of the subjective experience of aging. The aims of our study were to investigate views on aging (VA) as origins of age-related attributions of life changes and to investigate the implications of these age-related attributions for personal control (PC) and life satisfaction (LS).

Methods

Life changes and the attribution of life changes to age were independently assessed on a large international sample of older adults (N = 2,900; age range 40–90 years) from the Ageing as Future project. The valence of VA, PC, and LS were also assessed to investigate possible determinants (VA) and consequences (PC and LS) of age-related attributions of life changes.

Results

Attributions to age were shown to depend on the valence of experienced life changes, with more negative changes being linked to more age-related attributions. This relation was moderated by the valence of personally held VA, with more negative VA amplifying the relation between negative life changes and age-related attributions. Age-related attributions predicted reduced PC and lower LS and were found to exacerbate the effects of negative life changes on LS, especially for the older cohorts of our sample.

Discussion

Our findings help to better understand what determines age-related attributions of life changes and highlight the negative consequences of attributing them to aging. Age-related attributions of change are a major factor that worsens the subjective aging experience. Methodologically, our study emphasizes the necessity to separately assess changes and their attributions to age.
A Bayesian 3-D linear gravity inversion for complex density distributions: application to the Puysegur subduction system
Authors: Hightower Erin , Gurnis Michael , Van Avendonk Harm
Published: September 2020

We have developed a linear 3-D gravity inversion method capable of modelling complex geological regions such as subduction margins. Our procedure inverts satellite gravity to determine the best-fitting differential densities of spatially discretized subsurface prisms in a least-squares sense. We use a Bayesian approach to incorporate both data error and prior constraints based on seismic reflection and refraction data. Based on these data, Gaussian priors are applied to the appropriate model parameters as absolute equality constraints. To stabilize the inversion and provide relative equality constraints on the parameters, we utilize a combination of first and second order Tikhonov regularization, which enforces smoothness in the horizontal direction between seismically constrained regions, while allowing for sharper contacts in the vertical. We apply this method to the nascent Puysegur Trench, south of New Zealand, where oceanic lithosphere of the Australian Plate has underthrust Puysegur Ridge and Solander Basin on the Pacific Plate since the Miocene. These models provide insight into the density contrasts, Moho depth, and crustal thickness in the region. The final model has a mean standard deviation on the model parameters of about 17 kg m–3, and a mean absolute error on the predicted gravity of about 3.9 mGal, demonstrating the success of this method for even complex density distributions like those present at subduction zones. The posterior density distribution versus seismic velocity is diagnostic of compositional and structural changes and shows a thin sliver of oceanic crust emplaced between the nascent thrust and the strike slip Puysegur Fault. However, the northern end of the Puysegur Ridge, at the Snares Zone, is predominantly buoyant continental crust, despite its subsidence with respect to the rest of the ridge. These features highlight the mechanical changes unfolding during subduction initiation.
Fully discrete finite element approximation of the stochastic Cahn–Hilliard–Navier–Stokes system
Authors: Deugoué G , Moghomye B Jidjou , Tachim Medjo T
Published: September 2020

In this paper we study the numerical approximation of the stochastic Cahn–Hilliard–Navier–Stokes system on a bounded polygonal domain of $\mathbb{R}^{d}$, $d=2,3$. We propose and analyze an algorithm based on the finite element method and a semiimplicit Euler scheme in time for a fully discretization. We prove that the proposed numerical scheme satisfies the discrete mass conservative law, has finite energies and constructs a weak martingale solution of the stochastic Cahn–Hilliard–Navier–Stokes system when the discretization step (both in time and in space) tends to zero.
A Class of Fully Nonlinear Equations Arising in Conformal Geometry
Authors: Chen Li , Guo Xi , He Yan
Published: September 2020

In this paper, we consider the equations of Krylov type in conformal geometry on closed smooth Riemannian manifolds, which can be viewed as an extension of $\sigma _k$-Yamabe equation. Moreover, we prove local gradient and 2nd-derivative estimates for solutions to these equations and establish an existence result.
Optimizing a literature surveillance strategy to retrieve sound overall prognosis and risk assessment model papers
Authors: Kavanagh Patricia L , Frater Francine , Navarro Tamara , LaVita Peter , Parrish Rick , Iorio Alfonso
Published: September 2020

Objective

Our aim was to develop an efficient search strategy for prognostic studies and clinical prediction guides (CPGs), optimally balancing sensitivity and precision while independent of MeSH terms, as relying on them may miss the most current literature.

Materials and Methods

We combined 2 Hedges-based search strategies, modified to remove MeSH terms for overall prognostic studies and CPGs, and ran the search on 269 journals. We read abstracts from a random subset of retrieved references until ≥ 20 per journal were reviewed and classified them as positive when fulfilling standardized quality criteria, thereby assembling a standard dataset used to calibrate the search strategy. We determined performance characteristics of our new search strategy against the Hedges standard and performance characteristics of published search strategies against the standard dataset.

Results

Our search strategy retrieved 16 089 references from 269 journals during our study period. One hundred fifty-four journals yielded ≥ 20 references and ≥ 1 prognostic study or CPG. Against the Hedges standard, the new search strategy had sensitivity/specificity/precision/accuracy of 84%/80%/2%/80%, respectively. Existing published strategies tested against our standard dataset had sensitivities of 36%–94% and precision of 5%–10%.

Discussion

We developed a new search strategy to identify overall prognosis studies and CPGs independent of MeSH terms. These studies are important for medical decision-making, as they identify specific populations and individuals who may benefit from interventions.

Conclusion

Our results may benefit literature surveillance and clinical guideline efforts, as our search strategy performs as well as published search strategies while capturing literature at the time of publication.
Fine mapping genetic variants associated with age at puberty and sow fertility using SowPro90 genotyping array
Authors: Wijesena Hiruni R , Kachman Stephen D , Lents Clay A , Riethoven Jean-Jack , Trenhaile-Grannemann Melanie D , Safranski Tim J , Spangler Matthew L , Ciobanu Daniel C
Published: September 2020

Sow fertility traits, such as litter size and the number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable and expressed late in life. Age at puberty (AP) is an early indicator of reproductive longevity. Here, we utilized a custom Affymetrix single-nucleotide polymorphisms (SNPs) array (SowPro90) enriched with positional candidate genetic variants for AP and a haplotype-based genome-wide association study to fine map the genetic sources associated with AP and other fertility traits in research (University of Nebraska-Lincoln [UNL]) and commercial sow populations. Five major quantitative trait loci (QTL) located on four Sus scrofa chromosomes (SSC2, SSC7, SSC14, and SSC18) were discovered for AP in the UNL population. Negative correlations (r = −0.96 to −0.10; P < 0.0001) were observed at each QTL between genomic estimated breeding values for AP and reproductive longevity measured as lifetime number of parities (LTNP). Some of the SNPs discovered in the major QTL regions for AP were located in candidate genes with fertility-associated gene ontologies (e.g., P2RX3, NR2F2, OAS1, and PTPN11). These SNPs showed significant (P < 0.05) or suggestive (P < 0.15) associations with AP, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. For example, in the UNL population, when the number of favorable alleles of an SNP located in the 3′ untranslated region of PTPN11 (SSC14) increased, AP decreased (P < 0.0001), while LTNP increased (P < 0.10). Additionally, a suggestive difference in the observed NR2F2 isoforms usage was hypothesized to be the source of the QTL for puberty onset mapped on SSC7. It will be beneficial to further characterize these candidate SNPs and genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect the phenotypic variation of fertility traits.
Reimagining disability: the screening of donor gametes and embryos in IVF
Authors: Karpin Isabel , Mykitiuk Roxanne
Published: September 2020

In this article, we examine how disability is figured in the imaginaries that are given shape by the reproductive projects and parental desires facilitated by the bio-medical techniques and practices of assisted reproductive technologies (ARTs) that involve selection and screening for disability. We investigate how some users of ARTs understand and deploy these imaginaries in ways that are both concordant with and resistant to the understanding of disability embedded within the broader sociotechnical and social imaginaries. It is through users’ deliberations, choices, responses, and expectations that we come to understand how these imaginaries are perpetuated and resisted, and how maintaining them is also dependent upon the individual actions and actors who have internalized them. Our examination is grounded in a close analysis of a small selection of interviews drawn from data gathered during a 4-year project funded by the Australian Research Council exploring the Australian experience of cross border reproductive treatment, looking particularly at surrogacy, and gamete and embryo donation. Our interviewees were individuals or couples who used gamete or embryo donation, coupled at times with surrogacy in attempting to have a child. Participants discussed their views on testing, screening, and future disability.
Serum Concentrations of Per- and Polyfluoroalkyl Substances and Risk of Renal Cell Carcinoma
Authors: Shearer Joseph J , Callahan Catherine L , Calafat Antonia M , Huang Wen-Yi , Jones Rena R , Sabbisetti Venkata S , Freedman Neal D , Sampson Joshua N , Silverman Debra T , Purdue Mark P , Hofmann Jonathan N
Published: September 2020

Background

Per- and polyfluoroalkyl substances (PFAS) are highly persistent chemicals that have been detected in the serum of over 98% of the US population. Studies among highly exposed individuals suggest an association with perfluorooctanoic acid (PFOA) exposure and kidney cancer. It remains unclear whether PFOA or other PFAS are renal carcinogens or if they influence risk of renal cell carcinoma (RCC) at concentrations observed in the general population.

Methods

We measured prediagnostic serum concentrations of PFOA and 7 additional PFAS in 324 RCC cases and 324 individually matched controls within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Multivariable conditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CIs) relating serum PFAS concentrations and RCC risk. Individual PFAS were modeled continuously (log2-transformed) and categorically, with adjustment for kidney function and additional potential confounders. All statistical tests were 2-sided.

Results

We observed a positive association with RCC risk for PFOA (doubling in serum concentration, ORcontinuous = 1.71, 95% CI = 1.23 to 2.37, P = .002) and a greater than twofold increased risk among those in the highest quartile vs the lowest (OR = 2.63, 95% CI = 1.33 to 5.20, Ptrend = .007). The association with PFOA was similar after adjustment for other PFAS (ORcontinuous = 1.68, 95% CI = 1.07 to 2.63, P = .02) and remained apparent in analyses restricted to individuals without evidence of diminished kidney function and in cases diagnosed 8 or more years after phlebotomy.

Conclusions

Our findings add substantially to the weight of evidence that PFOA is a renal carcinogen and may have important public health implications for the many individuals exposed to this ubiquitous and highly persistent chemical.
Predicted Chemotherapy Benefit for Breast Cancer Patients With Germline Pathogenic Variants in Cancer Susceptibility Genes
Authors: Kurian Allison W , Ward Kevin C , Abrahamse Paul , Hamilton Ann S , Katz Steven J
Published: September 2020

Breast cancer patients increasingly undergo genetic testing. To examine chemotherapy indications for germline pathogenic variant (PV) carriers, we linked results of germline testing to Georgia and California Surveillance, Epidemiology, and End Results registry records, including 21-gene recurrence score (RS) results, for breast cancer patients diagnosed in 2013-2017. All statistical tests were 2-sided. Patients (N=37 349) had RS results of whom 714 had BRCA1, BRCA2, CHEK2, ATM, PALB2, or Lynch syndrome (MLH1, MSH2, MSH6, PMS2) PVs. For women aged 50 years or older at breast cancer diagnosis, RS often exceeded the chemotherapy benefit threshold (≥26) with BRCA1 (71.7% vs 14.4% with none; P <.001), PALB2 (37.1%; P = .001), and BRCA2 (44.3%; P < .001) PVs. Results were similar for women diagnosed at younger than 50 years of age. PVs in BRCA1, but not BRCA2, PALB2, ATM, CHEK2, or Lynch syndrome genes, were associated with elevated RS on multivariable analysis (P < .001). Results may inform RS testing decisions in breast cancer patients with PVs.
LncRNA BC083743 Promotes the Proliferation of Schwann Cells and Axon Regeneration Through miR-103-3p/BDNF After Sciatic Nerve Crush
Authors: Gao Lin , Feng Aiqin , Yue Peijian , Liu Yue , Zhou Qiaoyu , Zang Qiuling , Teng Junfang
Published: September 2020

To investigate the underlying mechanism of lncRNA BC083743 in regulating the proliferation of Schwann cells (SCs) and axon regeneration after sciatic nerve crush (SNC), we used a rat model. Sciatic function index and the atrophy ratio of gastrocnemius muscle were evaluated. The relationship among BC083743, miR-103-3p, and brain-derived neurotrophic factor (BDNF) and their regulation mechanism in the repair of SNC were investigated using in vivo and in vitro experiments. The expression changes of BC083743 were positively associated with that of BDNF following SNC, but the expression changes of miR-103-3p were inversely associated with that of BDNF. The SC proliferation and BDNF expression could be promoted by overexpression of BC083743, while they were inhibited by a miR-103-3p mimic. In addition, BC083743 interacted with and regulated miR-103-3p, thereby promoting BDNF expression and SC proliferation. BC083743 overexpression also promoted axon regeneration through miR-103-3p. In vivo experiments also indicated that BC083743 overexpression promoted the repair of SNC. In conclusion, LncRNA BC083743 promotes SC proliferation and the axon regeneration through miR-103-3p/BDNF after SNC.
A dummy-run evaluation of postoperative hypofractionated intensity-modulated radiation therapy (POHIM-RT) trials for cervical cancer
Authors: Cho Won Kyung , Kim Heejung , Park Won , Kim Sang-Won , Kim Jongwon , Lee Kang Kyu , Oh Jeong Geun , Yoon Mee Sun , Song Ju-Young , Ahn Ki Jung , Park Sung Kwang , Choi Jin Hwa , Bak Jino
Published: September 2020

The postoperative hypofractionated intensity-modulated radiation therapy (POHIM-RT) trial is a phase II study to evaluate toxicity following hypofractionated intensity modulated radiation therapy (IMRT) for cervical cancer. This study describes the results of a benchmark procedure for RT quality assurance of the POHIM-RT trial. Six participating institutions were provided computed tomography for RT planning and an IMRT plan for a sample and were instructed to delineate volumes, create a treatment plan and quality assurance (QA) plan, and submit the results of all procedures. The inter-institutional agreements on RT volume and plan results were evaluated using the kappa value and dice similarity coefficients. The simultaneous truth and performance level estimation (STAPLE) method was employed to generate a consensus target volume. The treatment volumes, organs-at-risk volumes, and results of the RT plan and QA reported by the institutions were acceptable and adhered well to the protocol. In terms of clinical target volume (CTV) delineation, there were differences between the institutions, particularly in vaginal cuff and paracolpium subsites. Consensus CTV was generated from the collected CTVs with the STAPLE method. The participating institutions showed considerable agreement regarding volume, dose and QA results. To improve CTV agreement in CTV, we provided feedback with images of the consensus target volume and detailed written guidelines for specific subsites that were the most heterogeneous.
A rare and severe case of pronator teres syndrome
Authors: Moura Francisco Serra E , Agarwal Anil
Published: September 2020

We present the case of a patient with severe symptoms of proximal forearm median nerve neuropathy. Over the course of 5 years his condition progressed to encompass rare features of combined pronator teres syndrome (PTS) and anterior interosseous nerve syndrome (AINS). The aetiology was found to be pronator teres compression and was managed successfully by surgical decompression. Proximal forearm median nerve compression should be considered as a continuum with two classic endpoints. At one end of the spectrum pure PTS presents with solely or mainly sensory symptoms, whereas at the other end AINS presents with pure motor symptoms. Hence, all possible anatomical sites of compression must be surgically explored in all cases of PTS or AINS, regardless of symptomatology. Timely referral to an experienced specialist is encouraged to ensure good outcomes, whenever a primary care practitioner encounters an atypical carpal tunnel syndrome-like presentation.
Why are second-generation transgenic crops not yet available in the market?
Authors: Chan R L , Trucco F , Otegui M E
Published: September 2020

The reasons behind the lack of second-generation transgenic crops in the market are explained by reinforcing multidisciplinary approaches, and redefining the concept of target environment.
Reflections on the Development of Digital Humanities
Authors: Orlandi Tito
Published: September 2020

Lecture presented to the Utrecht Conference of ADHO, 2019: my experience in the field of Humanities Computing/Digital Humanities, collocated in historical perspective, listing and briefly commenting what I have learned to be the essential theories which form our discipline. For this purpose, the fundamental disciplines are proposed, and their role in the discipline: computing theory, information and communication, formalization, algorithms and recursion; and, from humanities side, cybernetics, linguistics, semiotics, relational model, systems theory, modelization.
Founded semantics and constraint semantics of logic rules
Authors: Liu Yanhong A , Stoller Scott D
Published: September 2020

Logic rules and inference are fundamental in computer science and have been studied extensively. However, prior semantics of logic languages can have subtle implications and can disagree significantly, on even very simple programs, including in attempting to solve the well-known Russell’s paradox. These semantics are often non-intuitive and hard-to-understand when unrestricted negation is used in recursion. This paper describes a simple new semantics for logic rules, founded semantics, and its straightforward extension to another simple new semantics, constraint semantics, that unify the core of different prior semantics. The new semantics support unrestricted negation, as well as unrestricted existential and universal quantifications. They are uniquely expressive and intuitive by allowing assumptions about the predicates, rules and reasoning to be specified explicitly, as simple and precise binary choices. They are completely declarative and relate cleanly to prior semantics. In addition, founded semantics can be computed in linear time in the size of the ground program.
On uniform belief revision
Authors: Aravanis Theofanis
Published: September 2020

Rational belief-change policies are encoded in the so-called AGM revision functions, defined in the prominent work of Alchourrón, Gärdenfors and Makinson. The present article studies an interesting class of well-behaved AGM revision functions, called herein uniform-revision operators (or UR operators, for short). Each UR operator is uniquely defined by means of a single total preorder over all possible worlds, a fact that in turn entails a significantly lower representational cost, relative to an arbitrary AGM revision function, and an embedded solution to the iterated-revision problem, at no extra representational cost. Herein, we first demonstrate how weaker, more expressive—yet, more representationally expensive—types of uniform revision can be defined. Furthermore, we prove that UR operators, essentially, generalize a significant type of belief change, namely, parametrized-difference revision. Lastly, we show that they are (to some extent) relevance-sensitive, as well as that they respect the so-called principle of kinetic consistency.
Decomposing the internal faraday rotation of black hole accretion flows
Authors: Ricarte Angelo , Prather Ben S , Wong George N , Narayan Ramesh , Gammie Charles , Johnson Michael D
Published: September 2020

Faraday rotation has been seen at millimeter wavelengths in several low-luminosity active galactic nuclei, including Event Horizon Telescope (EHT) targets M87* and Sgr A*. The observed rotation measure (RM) probes the density, magnetic field, and temperature of material integrated along the line of sight. To better understand how accretion disc conditions are reflected in the RM, we perform polarized radiative transfer calculations using a set of general relativistic magnetohydrodynamic (GRMHD) simulations appropriate for M87*. We find that in spatially resolved millimetre wavelength images on event horizon scales, the RM can vary by orders of magnitude and even flip sign. The observational consequences of this spatial structure include significant time-variability, sign-flips, and non-λ2 evolution of the polarization plane. For some models, we find that internal RM can cause significant bandwidth depolarization even across the relatively narrow fractional bandwidths observed by the EHT. We decompose the linearly polarized emission in these models based on their RM and find that emission in front of the mid-plane can exhibit orders of magnitude less Faraday rotation than emission originating from behind the mid-plane or within the photon ring. We confirm that the spatially unresolved (i.e. image integrated) RM is a poor predictor of the accretion rate, with substantial scatter stemming from time variability and inclination effects. Models can be constrained with repeated observations to characterize time variability and the degree of non-λ2 evolution of the polarization plane.
AMICO galaxy clusters in KiDS-DR3: galaxy population properties and their redshift dependence
Authors: Radovich Mario , Tortora Crescenzo , Bellagamba Fabio , Maturi Matteo , Moscardini Lauro , Puddu Emanuella , Roncarelli Mauro , Roy Nivya , Bardelli Sandro , Marulli Federico , Sereno Mauro , Getman Fedor , Napolitano Nicola R
Published: September 2020

A catalogue of galaxy clusters was obtained in an area of 414 $\deg ^2$ up to a redshift z ∼ 0.8 from the Data Release 3 of the Kilo-Degree Survey (KiDS-DR3), using the Adaptive Matched Identifier of Clustered Objects (amico) algorithm. The catalogue and the calibration of the richness–mass relation were presented in two companion papers. Here, we describe the selection of the cluster central galaxy and the classification of blue and red cluster members, and analyse the main cluster properties, such as the red/blue fraction, cluster mass, brightness, and stellar mass of the central galaxy, and their dependence on redshift and cluster richness. We use the Illustris-TNG simulation, which represents the state-of-the-art cosmological simulation of galaxy formation, as a benchmark for the interpretation of the results. A good agreement with simulations is found at low redshifts (z ≤ 0.4), while at higher redshifts the simulations indicate a lower fraction of blue galaxies than what found in the KiDS-amico catalogue: we argue that this may be due to an underestimate of star-forming galaxies in the simulations. The selection of clusters with a larger magnitude difference between the two brightest central galaxies, which may indicate a more relaxed cluster dynamical status, improves the agreement between the observed and simulated cluster mass and stellar mass of the central galaxy. We also find that at a given cluster mass the stellar mass of blue central galaxies is lower than that of the red ones.
Correlation between optical and γ-ray flux variations in bright flat spectrum radio quasars
Authors: Rajput Bhoomika , Stalin C S , Sahayanathan S
Published: September 2020

Blazars are known to show flux variations over a range of energies from low-energy radio to high-energy γ-rays. Cross-correlation analysis of the optical and γ-ray light curves in blazars shows that flux variations are generally correlated in both bands, however, there are exceptions. We explored this optical–GeV connection in four flat spectrum radio quasars by a systematic investigation of their long-term optical and γ-ray light curves. On analysis of the four sources, namely 3C 273, 3C 279, PKS 1510−089, and CTA 102, we noticed different behaviours between the optical and GeV flux variations. We found instances when (i) the optical and GeV flux variations are closely correlated, (ii) there are optical flares without γ-ray counterparts, and (iii) γ-ray flares without optical counterparts. To understand these diverse behaviours, we carried out broad-band spectral energy distribution (SED) modelling of the sources at different epochs using a one-zone leptonic emission model. The optical–UV emission is found to be dominated by emission from the accretion disc in the sources PKS 1510−089, CTA 102, and 3C 273, while in 3C 279, the synchrotron radiation from the jet dominates the optical–UV emission. Our SED analysis indicates that (i) correlated optical and γ-ray flux variations are caused by changes in the bulk Lorentz factor (Γ), (ii) γ-ray flares without optical counterparts are due to increase in Γ and/or the electron energy density, and (iii) an optical flare without γ-ray counterpart is due to increase in the magnetic field strength.
A spectral study of the black hole X-ray binary MAXI J1820+070 with AstroSat and NuSTAR
Authors: Chakraborty Sudip , Navale Nilam , Ratheesh Ajay , Bhattacharyya Sudip
Published: September 2020

MAXI J1820+070 is a newly discovered transient black hole X-ray binary, which showed several spectral and temporal features. In this work, we analyse the broad-band X-ray spectra from all three simultaneously observing X-ray instruments onboard AstroSat, as well as contemporaneous X-ray spectra from NuSTAR, observed during the hard state of MAXI J1820+070 in 2018 March. Implementing a combination of multicolour disc model, relativistic blurred reflection model relxilllpcp, and a distant reflection in the form of xillvercp, we achieve reasonable and consistent fits for AstroSat and NuSTAR spectra. The best-fitting model suggests a low temperature disc (kTin ∼ 0.3 keV), iron overabundance (AFe ∼ 4–5 solar), a short lamp-post corona height (h ≲ 8Rg), and a high corona temperature (kTe ∼ 115–150 keV). Addition of a second Comptonization component leads to a significantly better fit, with the kTe of the second Comptonization component being ∼14–18 keV. Our results from independent observations with two different satellites in a similar source state indicate an inhomogeneous corona, with decreasing temperature attributed to increasing height. Besides, utilizing the broader energy coverage of AstroSat, we estimate the black hole mass to be 6.7–13.9 M⊙, consistent with independent measurements reported in the literature.
SHαDE: survey description and mass–kinematics scaling relations for dwarf galaxies
Authors: Barat Dilyar , D’Eugenio Francesco , Colless Matthew , Sweet Sarah M , Groves Brent , Cortese Luca
Published: September 2020

The Study of H α from Dwarf Emissions (SHαDE) is a high spectral resolution (R = 13 500) H α integral field survey of 69 dwarf galaxies with stellar masses 106 < M⋆ < 109 M⊙. The survey used FLAMES on the ESO Very Large Telescope. SHαDE is designed to study the kinematics and stellar populations of dwarf galaxies using consistent methods applied to massive galaxies and at matching level of detail, connecting these mass ranges in an unbiased way. In this paper, we set out the science goals of SHαDE, describe the sample properties, outline the data reduction, and analysis processes. We investigate the log M⋆–log S0.5 mass–kinematics scaling relation, which has previously shown potential for combining galaxies of all morphologies in a single scaling relation. We extend the scaling relation from massive galaxies to dwarf galaxies, demonstrating this relation is linear down to a stellar mass of M⋆ ∼ 108.6 M⊙. Below this limit, the kinematics of galaxies inside one effective radius appears to be dominated by the internal velocity dispersion limit of the H α-emitting gas, giving a bend in the log M⋆–log S0.5 relation. Replacing stellar mass with total baryonic mass using gas mass estimate reduces the severity but does not remove the linearity limit of the scaling relation. An extrapolation to estimate the galaxies’ dark matter halo masses, yields a log Mh–log S0.5 scaling relation that is free of any bend, has reduced curvature over the whole mass range, and brings galaxies of all masses and morphologies on to the virial relation.
Observational signatures of disc and jet misalignment in images of accreting black holes
Authors: Chatterjee K , Younsi Z , Liska M , Tchekhovskoy A , Markoff S B , Yoon D , van Eijnatten D , Hesp C , Ingram A , van der Klis M B M
Published: September 2020

Black hole (BH) accretion is one of nature’s most efficient energy extraction processes. When gas falls in, a significant fraction of its gravitational binding energy is either converted into radiation or flows outwards in the form of BH-driven jets and disc-driven winds. Recently, the Event Horizon Telescope (EHT), an Earth-sized submillimetre radio interferometer, captured the first images of M87’s BH. These images were analysed and interpreted using general relativistic magnetohydrodynamics (GRMHD) models of accretion discs with rotation axes aligned with the BH spin axis. However, since infalling gas is often insensitive to the BH spin direction, misalignment between accretion disc and BH spin may be a common occurrence in nature. In this work, we use the general relativistic radiative transfer code bhoss to calculate the first synthetic radio images of (highly) tilted disc/jet models generated by our GPU-accelerated GRMHD code h-amr . While the tilt does not have a noticeable effect on the system dynamics beyond a few tens of gravitational radii from the BH, the warping of the disc and jet can imprint observable signatures in EHT images on smaller scales. Comparing the images from our GRMHD models to the 43 and 230 GHz EHT images of M87, we find that M87 may feature a tilted disc/jet system. Further, tilted discs and jets display significant time variability in the 230 GHz flux that can be further tested by longer-duration EHT observations of M87.
Young stellar cluster dilution near supermassive black holes: the impact of vector resonant relaxation on neighbour separation
Authors: Giral Martínez Juan , Fouvry Jean-Baptiste , Pichon Christophe
Published: September 2020

We investigate the rate of orbital orientation dilution of young stellar clusters in the vicinity of supermassive black holes. Within the framework of vector resonant relaxation, we predict the time evolution of the two-point correlation function of the stellar orbital plane orientations as a function of their initial angular separation and diversity in orbital parameters (semimajor axis, eccentricity). As expected, the larger the spread in initial orientations and orbital parameters, the more efficient the dilution of a given set of co-eval stars, with a characteristic time-scale set up by the coherence time of the background potential fluctuations. A Markovian prescription that matches numerical simulations allows us to efficiently probe the underlying kinematic properties of the unresolved nucleus when requesting consistency with a given dilution efficiency, imposed by the observed stellar disc within the 1 arcsec of Sgr A*. As a proof of concept, we compute maps of constant dilution times as a function of the semimajor axis cusp index and fraction of intermediate-mass black holes in the old background stellar cluster. This computation suggests that vector resonant relaxation should prove useful in this context since it impacts orientations on time-scales comparable to the stars’ age.
Evaluating the Performance of Malaria Genetics for Inferring Changes in Transmission Intensity Using Transmission Modeling
Authors: Watson Oliver J , Okell Lucy C , Hellewell Joel , Slater Hannah C , Unwin H Juliette T , Omedo Irene , Bejon Philip , Snow Robert W , Noor Abdisalan M , Rockett Kirk , Hubbart Christina , Nankabirwa Joaniter I , Greenhouse Bryan , Chang Hsiao-Han , Ghani Azra C , Verity Robert
Published: September 2020

Substantial progress has been made globally to control malaria, however there is a growing need for innovative new tools to ensure continued progress. One approach is to harness genetic sequencing and accompanying methodological approaches as have been used in the control of other infectious diseases. However, to utilize these methodologies for malaria, we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment, which all impact the level of genetic diversity and relatedness of malaria parasites. We develop an individual-based transmission model to simulate malaria parasite genetics parameterized using estimated relationships between complexity of infection and age from five regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterize the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The model predicted malaria prevalence with a mean absolute error of 0.055. Different assumptions about the availability of sample metadata were considered, with the most accurate predictions of malaria prevalence made when the clinical status and age of sampled individuals is known. Parasite genetics may provide a novel surveillance tool for estimating the prevalence of malaria in areas in which prevalence surveys are not feasible. However, the findings presented here reinforce the need for patient metadata to be recorded and made available within all future attempts to use parasite genetics for surveillance.
Ecological Load and Balancing Selection in Circumboreal Barnacles
Authors: Nunez Joaquin C B , Rong Stephen , Damian-Serrano Alejandro , Burley John T , Elyanow Rebecca G , Ferranti David A , Neil Kimberly B , Glenner Henrik , Rosenblad Magnus Alm , Blomberg Anders , Johannesson Kerstin , Rand David M
Published: September 2020

Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here, we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 My of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.