bluuebunny/crossref_metadata_2025 huggingface dataset:
A probabilistic approach to phase calibration – I. Effects of source structure on fringe-fitting
Authors: Natarajan I , Deane R , van Bemmel I , van Langevelde H J , Small D , Kettenis M , Paragi Z , Smirnov O , Szomoru A
Published: May 2020

We propose a probabilistic framework for performing simultaneous estimation of source structure and fringe-fitting parameters in very long baseline interferometry (VLBI) observations. As a first step, we demonstrate this technique through the analysis of synthetic short-duration Event Horizon Telescope observations of various geometric source models at 230 GHz, in the presence of baseline-dependent thermal noise. We perform Bayesian parameter estimation and model selection between the different source models to obtain reliable uncertainty estimates and correlations between various source and fringe-fitting related model parameters. We also compare the Bayesian posteriors with those obtained using widely used VLBI data reduction packages such as casa and aips, by fringe-fitting 200 Monte Carlo simulations of each source model with different noise realizations, to obtain distributions of the maximum a posteriori estimates. We find that, in the presence of resolved asymmetric source structure and a given array geometry, the traditional practice of fringe-fitting with a point source model yields appreciable offsets in the estimated phase residuals, potentially biasing or limiting the dynamic range of the starting model used for self-calibration. Simultaneously estimating the source structure earlier in the calibration process with formal uncertainties improves the precision and accuracy of fringe-fitting and establishes the potential of the available data, especially when there is little prior information. We also note the potential applications of this method to astrometry and geodesy for specific science cases and the planned improvements to the computational performance and analyses of more complex source distributions.
A framework for measuring weak-lensing magnification using the Fundamental Plane
Authors: Freudenburg Jenna K C , Huff Eric M , Hirata Christopher M
Published: June 2020

Galaxy–galaxy lensing is an essential tool for probing dark matter haloes and constraining cosmological parameters. While galaxy–galaxy lensing measurements usually rely on shear, weak-lensing magnification contains additional constraining information. Using the Fundamental Plane (FP) of elliptical galaxies to anchor the size distribution of a background population is one method that has been proposed for performing a magnification measurement. We present a formalism for using the FP residuals of elliptical galaxies to jointly estimate the foreground mass and background redshift errors for a stacked lens scenario. The FP residuals include information about weak-lensing magnification κ, and therefore foreground mass, since to first order, non-zero κ affects galaxy size but not other FP properties. We also present a modular, extensible code that implements the formalism using emulated galaxy catalogues of a photometric galaxy survey. We find that combining FP information with observed number counts of the source galaxies constrains mass and photo-z error parameters significantly better than an estimator that includes number counts only. In particular, the constraint on the mass is 17.0 per cent if FP residuals are included, as opposed to 27.7 per cent when only number counts are included. The effective size noise for a foreground lens of mass $M_\mathrm{ H}=10^{14}\, \mathrm{M}_\odot$, with a conservative selection function in size and surface brightness applied to the source population, is σκ, eff = 0.250. We discuss the improvements to our FP model necessary to make this formalism a practical companion to shear analyses in weak-lensing surveys.
The Galactic radial abundance gradients of C, N, O, Ne, S, Cl, and Ar from deep spectra of H ii regions
Authors: Arellano-Córdova K Z , Esteban C , García-Rojas J , Méndez-Delgado J E
Published: May 2020

We present a reassessment of the radial abundance gradients of C, N, O, Ne, S, Cl, and Ar in the Milky Way using deep spectra of 33 H ii regions gathered from the literature, covering Galactocentric distances from 6 to 17 kpc. The distances of the objects have been revised using Gaia parallaxes. We recalculate the physical conditions and ionic abundances in an homogeneous way using updated atomic data. All the objects have direct determination of the electron temperature, permitting to derive their precise ionic abundances. We analyse and compare different ICF schemes for each element in order to obtain the most confident total abundances. Due to the revised distances, our results do not support previous claims about a possible flattening of the O/H gradient in the inner Galactic disc. We find that the Galactic N/O gradient is rather flat, in contrast to what has been found in other spiral galaxies. The slope of the gradients of some elements is sensitive to the ICF scheme used, especially in the case of Ne. The dispersion around the fit for the gradients of C, N, O, S, Cl, and Ar is of the order of the typical uncertainties in the determination of the abundances, implying the absence of significant inhomogeneities in the chemical composition of the ionized gas phase of the ISM. We find flat gradients of log(S/O) and log(Cl/O) and very shallow or flat ones for log(Ne/O) and log(Ar/O), consistent with a lockstep evolution of Ne, S, Cl, and Ar with respect to O.
The nuclear architecture of NGC 4151: on the path toward a universal outflow mechanism in light of NGC 1068
Authors: May D , Steiner J E , Menezes R B , Williams D R A , Wang J
Published: June 2020

We report near-infrared integral field spectroscopic observations of the active galactic nucleus NGC 4151 with archive data from the NIFS-Gemini North Telescope. We have selected best-seeing observations (≲0.3 arcsec) that, allied to our methodology of image processing techniques, show structures with spatial resolution comparable to those of the HST. The intricate outflow of NGC 4151 is revisited in light of the results found for NGC 1068, in a previous work, and a very similar dynamic is found: the low-velocity [Fe ii] emission depicts the glowing walls of an hourglass structure, while the high-velocity gas fills its volume. From this finding, we show that the misalignment between the jet and the NLR is not a projection effect, as previously thought. A molecular outflow is detected for the first time in this galaxy and, just like in NGC 1068, the transition between the molecular and the ionized gas phases comes from the fragmentation of molecular cavity walls into bullets of ionized gas exposed to the central source. Furthermore, it is suggestive that the same geometrical dichotomy between the cones seen in NGC 1068 is found here, with one side, where the cavity is disrupted by the AGN, being more extended than the other. Finally, a new spatial correlation between the high-velocity [Fe ii] and the soft X-ray emission of [Ne ix] is found, which is unexpected given the difference between their ionization potentials.
Accretion disc luminosity for black holes surrounded by dark matter
Authors: Boshkayev K , Idrissov A , Luongo O , Malafarina D
Published: June 2020

We consider the observational properties of a static black hole space–time immersed in a dark matter envelope. We investigate how the modifications to geometry induced by the presence of dark matter affect the luminosity of the black hole’s accretion disc. We show that the same disc luminosity as produced by a black hole in vacuum may be produced by a smaller black hole surrounded by dark matter under certain conditions. In particular, we demonstrate that the luminosity of the disc is markedly altered by the presence of dark matter, suggesting that the mass estimation of distant supermassive black holes may be changed if they are immersed in dark matter. We argue that a similar effect holds in more realistic scenarios, and we discuss the refractive index related to dark matter lensing. Finally, we show how the results presented here may help to explain the observed luminosity of supermassive black holes in the early Universe.
Effects of the Hubble parameter on the cosmic growth of the first quasars
Authors: Nunes Rafael C , Pacucci Fabio
Published: June 2020

Supermassive black holes (SMBHs) play a crucial role in the evolution of galaxies and are currently detected up to $z$ ∼ 7.5. Theories describing black hole (BH) growth are challenged by how rapidly seeds with initial mass $M_\bullet \lesssim 10^5 \, {\rm M_\odot }$, formed at $z$ ∼ 20–30, grew to $M_\bullet \sim 10^9 \, {\rm M_\odot }$ by $z$ ∼ 7. Here we study the effects of the value of the Hubble parameter, H0, on models describing the early growth of BHs. First, we note that the predicted mass of a quasar at $z$ = 6 changes by $\gt 300{{\ \rm per\ cent}}$ if the underlying Hubble parameter used in the model varies from H0 = 65 to H0 = 74 km s−1Mpc−1, a range encompassing current estimates. Employing an MCMC approach based on priors from $z$ ≳ 6.5 quasars and on H0, we study the interconnection between H0 and the parameters describing BH growth: seed mass Mi and Eddington ratio fEdd. Assuming an Eddington ratio of fEdd = 0.7, in agreement with previous estimates, we find $H_0 = 73.6^{+1.2}_{-3.3}$ km s−1Mpc−1. In a second analysis, allowing all the parameters to vary freely, we find log (Mi/M⊙) > 4.5 (at 95 per cent CL), $H_0 = 74^{+1.5}_{-1.4}$ km s−1Mpc−1 and $f_{\rm Edd}=0.77^{+0.035}_{-0.026}$ at 68 per cent CL. Our results on the typical Eddington ratio are in agreement with previous estimates. Current values of the Hubble parameter strongly favour heavy seed formation scenarios, with $M_i \gtrsim 10^4 \, {\rm M_\odot }$. In our model, with the priors on BH masses of quasars used, light seed formation scenarios are rejected at ∼3σ.
Gamma-ray-emitting narrow-line Seyfert 1 galaxies: the Swift view
Authors: D’Ammando F
Published: June 2020

We report the analysis of all Swift observations available up to 2019 April of γ-ray-emitting narrow-line Seyfert 1 galaxies (NLSy1). The distribution of X-ray luminosities (and fluxes) indicates that the jet radiation significantly contributes to their X-ray emission, with Doppler boosting making values higher than other radio-loud NLSy1. The 0.3–10 keV photon indices are on average harder with respect to radio-quiet and radio-loud NLSy1, confirming a dominant jet contribution in X-rays. However, the lower variability amplitude with respect to blazars and the softening of the spectrum in some periods suggests that also the corona radiation contributes to the X-ray emission. In optical and ultraviolet (UV) significant flux changes have been observed on daily, weekly, and monthly time-scale, providing a clear indication of the significant contribution of the jet radiation in this part of spectrum. A strong correlation between X-ray, UV, and optical emission and simultaneous flux variations have been observed in 1H 0323+342, SBS 0846+513, PMN J0948+0022 as expected in case the jet radiation is the dominant mechanism. Correlated multiband variability favours the jet-dominated scenario also in FBQS J1644+2619 and PKS 2004−447. The summed X-ray Telescope spectra of 1H 0323+342, SBS 0846+513, PMN J0948+0022, and FBQS J1644+2619 are well fitted by a broken power law with a break around 2 keV. The spectrum above 2 keV is dominated by the non-thermal emission from a beamed relativistic jet, as suggested by the hard photon index. A Seyfert-like feature like the soft X-ray excess has been observed below 2 keV, making these γ-ray-emitting NLSy1 different from typical blazars.
Deep XMM–Newton observations of the most distant SPT-SZ galaxy cluster
Authors: Mantz Adam B , Allen Steven W , Morris R Glenn , Canning Rebecca E A , Bayliss Matthew , Bleem Lindsey E , Floyd Benjamin T , McDonald Michael
Published: June 2020

We present results from a 577 ks XMM–Newton observation of SPT-CL J0459–4947, the most distant cluster detected in the South Pole Telescope 2500 square degree (SPT-SZ) survey, and currently the most distant cluster discovered through its Sunyaev–Zel’dovich effect. The data confirm the cluster’s high redshift, z = 1.71 ± 0.02, in agreement with earlier, less precise optical/IR photometric estimates. From the gas density profile, we estimate a characteristic mass of $M_{500}=(1.8\pm 0.2)\times 10^{14}\, {\rm M}_{\odot }$; cluster emission is detected above the background to a radius of $\sim \!2.2\, r_{500}$, or approximately the virial radius. The intracluster gas is characterized by an emission-weighted average temperature of 7.2 ± 0.3 keV and metallicity with respect to Solar of $Z/\, Z_{\odot }=0.37\pm 0.08$. For the first time at such high redshift, this deep data set provides a measurement of metallicity outside the cluster centre; at radii $r\gt 0.3\, r_{500}$, we find $Z/\, Z_{\odot }=0.33\pm 0.17$ in good agreement with precise measurements at similar radii in the most nearby clusters, supporting an early enrichment scenario in which the bulk of the cluster gas is enriched to a universal metallicity prior to cluster formation, with little to no evolution thereafter. The leverage provided by the high redshift of this cluster tightens by a factor of 2 constraints on evolving metallicity models, when combined with previous measurements at lower redshifts.
Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation
Authors: Chen Meirong , Kuhle Bernhard , Diedrich Jolene , Liu Ze , Moresco James J , Yates III John R , Pan Tao , Yang Xiang-Lei
Published: May 2020

The accuracy in pairing tRNAs with correct amino acids by aminoacyl-tRNA synthetases (aaRSs) dictates the fidelity of translation. To ensure fidelity, multiple aaRSs developed editing functions that remove a wrong amino acid from tRNA before it reaches the ribosome. However, no specific mechanism within an aaRS is known to handle the scenario where a cognate amino acid is mischarged onto a wrong tRNA, as exemplified by AlaRS mischarging alanine to G4:U69-containing tRNAThr. Here, we report that the mischargeable G4:U69-containing tRNAThr are strictly conserved in vertebrates and are ubiquitously and abundantly expressed in mammalian cells and tissues. Although these tRNAs are efficiently mischarged, no corresponding Thr-to-Ala mistranslation is detectable. Mistranslation is prevented by a robust proofreading activity of ThrRS towards Ala-tRNAThr. Therefore, while wrong amino acids are corrected within an aaRS, a wrong tRNA is handled in trans by an aaRS cognate to the mischarged tRNA species. Interestingly, although Ala-tRNAThr mischarging is not known to occur in bacteria, Escherichia coli ThrRS also possesses robust cross-editing ability. We propose that the cross-editing activity of ThrRS is evolutionarily conserved and that this intrinsic activity allows G4:U69-containing tRNAThr to emerge and be preserved in vertebrates to have alternative functions without compromising translational fidelity.
Passion for an activity: a new predictor of sleep quality
Authors: Bélanger Jocelyn J , Raafat Karima A , Nisa Claudia F , Schumpe Birga M
Published: May 2020

Study Objectives

The present research examines the relationship between people’s frequent involvement in an activity they like and find important (i.e., a passion) and the quality of their sleep. Research on the dualistic model of passion has widely documented the relationship between individuals’ type of passion—harmonious versus obsessive—and the quality of their mental and physical health. However, research has yet to examine the relationship between passion and sleep quality. Building on prior research has shown that obsessive (vs harmonious) passion is related to depressive mood symptoms—an important factor associated with sleep problems—we hypothesized that obsessive passion would be associated with overall worse sleep quality, whereas harmonious passion would predict better sleep quality.

Methods

A sample of 1,506 Americans filled out an online questionnaire on sleep habits and passion. Sleep quality was measured using the Pittsburgh Sleep Quality Index. Hierarchical linear regressions and mediation analyses were carried out with results confirming our hypotheses.

Results

Obsessive passion for an activity was associated with worse sleep quality, whereas harmonious passion was associated with better sleep quality, adjusting for demographics, the type of passionate activity and its self-reported importance, alcohol and tobacco consumption, BMI, self-reported health, and diagnosed health conditions. The relationship between both types of passion and sleep quality was mediated by depressive mood symptoms.

Conclusions

Our study presents evidence of a strong relationship between sleep quality and passion, opening the door for future research to create new interventions to improve people’s sleep and, consequently, their well-being.
Distinct Neural Networks Relate to Common and Speaker-Specific Language Priors
Authors: Kroczek Leon O H , Gunter Thomas C
Published: May 2020

Effective natural communication requires listeners to incorporate not only very general linguistic principles which evolved during a lifetime but also other information like the specific individual language use of a particular interlocutor. Traditionally, research has focused on the general linguistic rules, and brain science has shown a left hemispheric fronto-temporal brain network related to this processing. The present fMRI research explores speaker-specific individual language use because it is unknown whether this processing is supported by similar or distinct neural structures. Twenty-eight participants listened to sentences of persons who used more easy or difficult language. This was done by manipulating the proportion of easy SOV vs. complex OSV sentences for each speaker. Furthermore, ambiguous probe sentences were included to test top-down influences of speaker information in the absence of syntactic structure information. We observed distinct neural processing for syntactic complexity and speaker-specific language use. Syntactic complexity correlated with left frontal and posterior temporal regions. Speaker-specific processing correlated with bilateral (right-dominant) fronto-parietal brain regions. Finally, the top-down influence of speaker information was found in frontal and striatal brain regions, suggesting a mechanism for controlled syntactic processing. These findings show distinct neural networks related to general language principles as well as speaker-specific individual language use.
Grower Records and Logistic Regression to Solve Production Problems in Highbush Blueberry
Authors: Besançon Thierry E. , Ward Daniel L. , Oudemans Peter V. , Pavlis Gary C.
Published: June 2020

Blueberry plants displaying abnormal fruit development in the form of splitting and equatorial russeting were reported from 15 farms in Atlantic and Burlington Counties, NJ, in the spring of 2017. The cause was unknown; however, phytotoxicity due to a chemical application was suspected. Grower application records were used to unravel the cause. A total of 237 records were received, of which 110 were from fields displaying injury. A logistic regression analysis identified pendimethalin as the primary cause, although soil type did show a probability greater than 1. Other incriminated herbicides were frequent tank mix partners with pendimethalin and not responsible for injury. The methodology described is helpful for identifying explanatory factors among a complex set of possible or likely causative elements. In this case pendimethalin was identified as the cause of blueberry phytotoxicity.
Lymphangioma in Childhood
Authors: Kalinova Krasimira , Georgiev Kaloyan , Doseva Sonya
Published: June 2020

The article presents a case of severe cervical lymphangioma of a young girl who undergoes combined operative and injection treatment. The types of therapeutic response, results, and nursing indications are discussed.
Effect of roux-en Y gastric bypass surgery on patients with type 2 diabetes mellitus
Authors: Chen Ke-Yan , Liu Ying-Li , Shang Jin-Cai , Su De-Wang , Yao Rong-Rong , Ke De-Zhi , Tian Hao
Published: June 2020

Background:

Previous studies have reported that roux-en Y gastric bypass surgery (RYGBS) can benefit patients with type 2 diabetes mellitus (T2DM). However, their conclusions are still inconsistent. Thus, this study will aim to assess the effect of RYGBS for patients with T2DM.

Methods:

In this study, the electronic databases of MEDLINE, EMBASE, CENTRAL, CINAHL, AMED, and CNKI from inceptions to the present without any limitations to language and publication status. All randomized controlled trials on assessing the effect of RYGBS for patients with T2DM will be included in this study. Two independent authors will carry out study search and selection according to the previous designed inclusion and exclusion criteria. At the same time, 2 authors will independently evaluate the risk of bias assessment by Cochrane risk of bias tool. Any disagreements between 2 authors will be solved by a third author through discussion. RevMan 5.3 software will be utilized for statistical analysis.

Results:

This study will summarize the most recent studies and will provide a deeper understanding about using the effect of RYGBS for patients with T2DM.

Conclusions:

The findings of this study will present the existing evidence for the effect of RYGBS for patients with T2DM.

Systematic review registration:

INPLASY202040127.
Effect of heat-clearing and detoxifying Chinese medicines combined with conventional therapy on mild hand, foot, and mouth disease with fever
Authors: Yan Shiyan , Lu Ying , Zhang Guoliang , Li Xiuhui , Wang Zhong , Yao Chen , Wu Guiyun , Luo Lin , Ai Yanke , Guo Zhongning , Li Hongjiao , Li Tao , Jia Zhenjun , Wang Junwen , He Liyun , Liu Baoyan
Published: June 2020

Background:

In China, heat-clearing and detoxifying Chinese medicines combined with conventional therapy are commonly applied to treat the mild hand, foot, and mouth disease (HFMD). However, there is lack of solid evidence on the efficacy and safety of such therapies.

Methods:

We conducted a pooled analysis with individual patient data from 5 strictly randomized controlled clinical trials to assess the efficacy and safety of this combination therapy for mild HFMD. An intention-to-treat analysis was performed. A 2-stage meta-analysis method was adopted to analyze the pooled effect size.

Results:

In total, 947 patients were included. Compared with conventional therapy, the combination therapy significantly reduced the progression rate of HFMD from mild to severe (odds ratio [OR] 0.43, 95% confidence interval [CI]: 0.22 to 0.83, P = .01). Meanwhile, the healing time of skin rash and oral ulcer in the combination therapy group was significantly shorter than that of conventional therapy. The overall hazard ratio (HR) of healing time of the skin rash or oral ulcer was 1.22 (95%CI: 1.04 to 1.43; P = .02). However, except Jinlianqingre effervescent tablets, the combination therapy cannot shorten the time to fever resolution (HR 1.12, 95%CI: 0.97 to 1.29, P = .14). Because of the heterogeneity, Jinlianqingre effervescent tablets were analyzed separately and the HRs of the time to fever resolution and the healing time of skin rash or oral ulcer were 3.88 (95%CI: 3.19 to 4.72; P < .0001) and 3.79 (95%CI: 2.81 to 5.11; P < .0001), respectively. There were 30 adverse events reported in total; 2 cases were related to Chinese medicines.

Conclusion:

In conclusion, the heat-clearing and detoxifying Chinese medicines on top of conventional therapy can effectively reduce the progressive rate of mild HFMD and improve healing of skin and oral mucosal lesions. More studies are needed for the time to fever resolution.
Introduction to special issue: ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’
Authors: Gopnik Alison , Frankenhuis Willem E. , Tomasello Michael
Published: May 2020

This special issue focuses on the relationship between life history and learning, especially during human evolution. ‘Life history’ refers to the developmental programme of an organism, including its period of immaturity, reproductive rate and timing, caregiving investment and longevity. Across many species an extended childhood and high caregiving investment appear to be correlated with particular kinds of plasticity and learning. Human life history is particularly distinctive; humans evolved an exceptionally long childhood and old age, and an unusually high level of caregiving investment, at the same time that they evolved distinctive capacities for cognition and culture. The contributors explore the relations between life history, plasticity and learning across a wide range of methods and populations, including theoretical and empirical work in biology, anthropology and developmental psychology.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
Life-history theory in psychology and evolutionary biology: one research programme or two?
Authors: Nettle Daniel , Frankenhuis Willem E.
Published: May 2020

The term ‘life-history theory’ (LHT) is increasingly often invoked in psychology, as a framework for integrating understanding of psychological traits into a broader evolutionary context. Although LHT as presented in psychology papers (LHT-P) is typically described as a straightforward extension of the theoretical principles from evolutionary biology that bear the same name (LHT-E), the two bodies of work are not well integrated. Here, through a close reading of recent papers, we argue that LHT-E and LHT-P are different research programmes in the Lakatosian sense. The core of LHT-E is built around ultimate evolutionary explanation, via explicit mathematical modelling, of how selection can drive divergent evolution of populations or species living under different demographies or ecologies. The core of LHT-P concerns measurement of covariation, across individuals, of multiple psychological traits; the proximate goals these serve; and their relation to childhood experience. Some of the links between LHT-E and LHT-P are false friends. For example, elements that are marginal in LHT-E are core commitments of LHT-P, and where explanatory principles are transferred from one to the other, nuance can be lost in transmission. The methodological rules for what grounds a prediction in theory are different in the two cases. Though there are major differences between LHT-E and LHT-P at present, there is much potential for greater integration in the future, through both theoretical modelling and further empirical research.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
The developmental support hypothesis: adaptive plasticity in neural development in response to cues of social support
Authors: Snell-Rood Emilie , Snell-Rood Claire
Published: May 2020

Across mammals, cues of developmental support, such as touching, licking or attentiveness, stimulate neural development, behavioural exploration and even overall body growth. Why should such fitness-related traits be so sensitive to developmental conditions? Here, we review what we term the ‘developmental support hypothesis’, a potential adaptive explanation of this plasticity. Neural development can be a costly process, in terms of time, energy and exposure. However, environmental variability may sometimes compromise parental care during this costly developmental period. We propose this environmental variation has led to the evolution of adaptive plasticity of neural and behavioural development in response to cues of developmental support, where neural development is stimulated in conditions that support associated costs. When parental care is compromised, offspring grow less and adopt a more resilient and stress-responsive strategy, improving their chances of survival in difficult conditions, similar to existing ideas on the adaptive value of early-life programming of stress. The developmental support hypothesis suggests new research directions, such as testing the adaptive value of reduced neural growth and metabolism in stressful conditions, and expanding the range of potential cues animals may attend to as indicators of developmental support. Considering evolutionary and ecologically appropriate cues of social support also has implications for promoting healthy neural development in humans.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
The adaptive origins of uniquely human sociality
Authors: Tomasello Michael
Published: May 2020

Humans possess some unique social-cognitive skills and motivations, involving such things as joint attention, cooperative communication, dual-level collaboration and cultural learning. These are almost certainly adaptations for humans' especially complex sociocultural lives. The common assumption has been that these unique skills and motivations emerge in human infancy and early childhood as preparations for the challenges of adult life, for example, in collaborative foraging. In the current paper, I propose that the curiously early emergence of these skills in infancy––well before they are needed in adulthood––along with other pieces of evidence (such as almost exclusive use with adults not peers) suggests that aspects of the evolution of these skills represent ontogenetic adaptations to the unique socio-ecological challenges human infants face in the context of a regime of cooperative breeding and childcare.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
Innovation, life history and social networks in human evolution
Authors: Sterelny Kim
Published: May 2020

There is a famous puzzle about the first 3 million years of archaeologically visible human technological history. The pace of change, of innovation and its uptake, is extraordinarily slow. In particular, the famous handaxes of the Acheulian technological tradition first appeared about 1.7 Ma, and persisted with little change until about 800 ka, perhaps even longer. In this paper, I will offer an explanation of that stasis based in the life history and network characteristics that we infer (on phylogenetic grounds) to have characterized earlier human species. The core ideas are that (i) especially in earlier periods of hominin evolution, we are likely to find archaeological traces only of widespread and persisting technologies and practices; (ii) the record is not a record of the rate of innovation, but the rate of innovations establishing in a landscape; (iii) innovations are extremely vulnerable to stochastic loss while confined to the communities in which they are made and established; (iv) the export of innovation from the local group is sharply constrained if there is a general pattern of hostility and suspicion between groups, or even if there is just little contact between adults of adjoining groups. That pattern is typical of great apes and likely, therefore, to have characterized at least early hominin social lives. Innovations are unlikely to spread by adult-to-adult interactions across community boundaries. (v) Chimpanzees and bonobos are characterized by male philopatry and subadult female dispersal; that is, therefore, the most likely early hominin pattern. If so, the only innovations at all likely to expand beyond the point of origin are those acquired by subadult females, and ones that can be expressed by those females, at high enough frequency and salience for them to spread, in the bands that the females join. These are very serious filters on the spread of innovation.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
The human life history is adapted to exploit the adaptive advantages of culture
Authors: Richerson Peter J. , Boyd Robert
Published: May 2020

Humans evolved from an ape ancestor that was highly intelligent, moderately social and moderately dependent on cultural adaptations for subsistence technology (tools). By the late Pleistocene, humans had become highly dependent on culture for subsistence and for rules to organize a complex social life. Adaptation by cultural traditions transformed our life history, leading to an extended juvenile period to learn subsistence and social skills, post-reproductive survival to help conserve and transmit skills, a dependence on social support for mothers of large-brained, very dependent and nutrient-demanding offspring, males devoting substantial effort to provisioning rather than mating, and the cultivation of large social networks to tap pools in information unavailable to less social species. One measure of the success of the exploitation of culture is that the minimum inter-birth interval of humans is nearly half that of our ape relatives. Another measure is the wide geographical distribution of humans compared with other apes, based on subsistence systems adapted to fine-scale spatial environmental variation. An important macro-evolutionary question is why our big-brained, culture-intensive life-history strategy evolved so recently and in only our lineage. We suggest that increasing spatial and temporal variation in the Pleistocene favoured cultural adaptations.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals'.
The optimal timing of teaching and learning across the life course
Authors: Gurven Michael D. , Davison Raziel J. , Kraft Thomas S.
Published: May 2020

The evolutionary biologist W. D. Hamilton (Hamilton 1966J. Theor. Biol.12, 12–45. (doi:10.1016/0022-5193(66)90184-6)) famously showed that the force of natural selection declines with age, and reaches zero by the age of reproductive cessation. However, in social species, the transfer of fitness-enhancing resources by postreproductive adults increases the value of survival to late ages. While most research has focused on intergenerational food transfers in social animals, here we consider the potential fitness benefits of information transfer, and investigate the ecological contexts where pedagogy is likely to occur. Although the evolution of teaching is an important topic in behavioural biology and in studies of human cultural evolution, few formal models of teaching exist. Here, we present a modelling framework for predicting the timing of both information transfer and learning across the life course, and find that under a broad range of conditions, optimal patterns of information transfer in a skills-intensive ecology often involve postreproductive aged teachers. We explore several implications among human subsistence populations, evaluating the cost of hunting pedagogy and the relationship between activity skill complexity and the timing of pedagogy for several subsistence activities. Long lifespan and extended juvenility that characterize the human life history likely evolved in the context of a skills-intensive ecological niche with multi-stage pedagogy and multigenerational cooperation.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
Cognitive consequences of our grandmothering life history: cultural learning begins in infancy
Authors: Hawkes Kristen
Published: May 2020

Postmenopausal longevity distinguishes humans from our closest living evolutionary cousins, the great apes, and may have evolved in our lineage when the economic productivity of grandmothers allowed mothers to wean earlier and overlap dependents. Since increased longevity retards development and expands brain size across the mammals, this hypothesis links our slower developing, bigger brains to ancestral grandmothering. If foraging interdependence favoured postmenopausal longevity because grandmothers' subsidies reduced weaning ages, then ancestral infants lost full maternal engagement while their slower developing brains were notably immature. With survival dependent on social relationships, sensitivity to reputations is wired very early in neural ontogeny, beginning our lifelong preoccupation with shared intentionality.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
Childhood as a solution to explore–exploit tensions
Authors: Gopnik Alison
Published: May 2020

I argue that the evolution of our life history, with its distinctively long, protected human childhood, allows an early period of broad hypothesis search and exploration, before the demands of goal-directed exploitation set in. This cognitive profile is also found in other animals and is associated with early behaviours such as neophilia and play. I relate this developmental pattern to computational ideas about explore–exploit trade-offs, search and sampling, and to neuroscience findings. I also present several lines of empirical evidence suggesting that young human learners are highly exploratory, both in terms of their search for external information and their search through hypothesis spaces. In fact, they are sometimes more exploratory than older learners and adults.

This article is part of the theme issue ‘Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals’.
A Simple Method of Finding an Approximate Pattern of the COVID-19 Spread
Authors: Baruah Hemanta Kumar
Published: May 2020

We are going to show that the pattern of spread of COVID-19 outside China is not monotonic. We have considered the data outside China because we are going to study the data starting from March 21, and by that time the spread had almost come to a stop in China. We have used for our analysis data on total cases outside China till April 25, 2020, and data from April 26 to April 30 for comparison of forecasts and observed values. Right from the beginning the spread pattern was nonlinear, and by the end of the third week of March the nonlinearity became nearly exponential. The exponential pattern thereafter has changed by around March 28, April 5, April 11 and April 18. Since March 21, the spread is following a nearly exponential pattern of growth changing observably at almost regular intervals of seven days. It is but natural that at some point of time the countries that had been contributing in observably large numbers to the total cases would start to show diminishing growth patterns. Therefore long term forecasts using our method would give us slightly overestimated results. However, for short term forecasting our simple method does work very well when we consider the total number of cases in the world and not in any particular country.
Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction
Authors: Greenstein R.A. , Ng Henry , Barrales Ramon R. , Tan Catherine , Braun Sigurd , Al-Sady Bassem
Published: May 2020

Heterochromatin spreading, the expansion of gene-silencing structures from DNA-encoded nucleation sites, occurs in distinct settings. Spreading re-establishes gene-poor constitutive heterochromatin every cell cycle, but also invades gene-rich euchromatin de novo to steer cell fate decisions. How chromatin context, i.e. euchromatic, heterochromatic, or different nucleator types, influences the determinants of this process remains poorly understood. By screening a nuclear function gene deletion library in fission yeast using a previously established heterochromatin spreading sensor system, we identified regulators that positively or negatively alter the propensity of a nucleation site to spread heterochromatin. We find that different chromatin contexts are dependent on unique sets of genes for the regulation of heterochromatin spreading. Further, we find that spreading in constitutive heterochromatin requires Clr6 histone deacetylase complexes containing the Fkh2 transcription factor, while the Clr3 deacetylase is globally required for silencing. Fkh2 acts by recruiting Clr6 to nucleation-distal chromatin sites. Our results segregate the pathways that control lateral heterochromatin spreading from those that instruct DNA-directed assembly in nucleation.
Decoding the role of CBLB for innate immune responses regulating systemic dissemination during Non-Tuberculous Mycobacteria infection
Authors: Mudalagiriyappa Srinivasu , Sharma Jaishree , Abdelaal Hazem F. M. , Kelly Thomas C. , Choi Woosuk , Vieson Miranda D. , Talaat Adel M. , Nanjappa Som G.
Published: May 2020

Non-Tuberculous Mycobacteria (NTM) are ubiquitous in nature, present in soil and water, and cause primary leading to disseminated infections in immunocompromised individuals. NTM infections are surging in recent years due to an increase in an immune-suppressed population, medical interventions, and patients with underlying lung diseases. Host regulators of innate immune responses, frontiers for controlling infections and dissemination, are poorly defined during NTM infections. Here, we describe the role of CBLB, an E3-ubiquitin ligase, for innate immune responses and disease progression in a mouse model of NTM infection under compromised T-cell immunity. We found that CBLB thwarted NTM growth and dissemination in a time- and infection route- dependent manner. Mechanistically, we uncovered defects in many innate immune cells in the absence ofCblb, including poor responses of NK cells, inflammatory monocytes, and conventional dendritic cells. Strikingly, Cblb-deficient macrophages were competent to control NTM growthin vitro. Histopathology suggested the lack of early formation of granulomatous inflammation in the absence of CBLB. Collectively, CBLB is essential to mount productive innate immune responses and help prevent the dissemination during an NTM infection under T-cell deficiency.
Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank
Authors: Venkataraman Guhan Ram , Olivieri Julia Eve , DeBoever Christopher , Tanigawa Yosuke , Justesen Johanne Marie , Dilthey Alexander , Rivas Manuel A.
Published: May 2020

The human leukocyte antigen (HLA) region is one of the most disease-associated regions of the human genome, yet even well-studied alleles in the HLA region have unknown impact on disease. Here, we study the effect of 156 HLA alleles on 677 binary phenotypes for 337,138 individuals in the UK Biobank. We assess HLA allele associations and subsequently use Bayesian Model Averaging for conditional analysis, a) replicating 88 known associations between HLA alleles and binary disease phenotypes such as cancer, and b) discovering 90 novel associations to phenotypes such as skin and reproductive tract cancers and to other phenotypes not previously associated with the HLA region (e.g. anemias and acne). We find several non-additive effects, suggesting a more complex landscape of disease-modifying effects throughout the region. Finally, we discover associations between homozygous HLA allele burden and several cancer and other phenotypes, suggesting that peptide presentation spectra as coded for by the HLA region are important in determining disease risk. Our results demonstrate the HLA region’s complexity and richness while underscoring its clinical relevance.
CREBBPandSTAT6co-mutation and 16p13 and 1p36 loss define the t(14;18)-negative diffuse variant of follicular lymphoma
Authors: Xian Rena R. , Xie Yi , Haley Lisa M. , Yonescu Raluca , Pallavajjala Aparna , Pittaluga Stefania , Jaffe Elaine S. , Duffield Amy S. , McCall Chad M. , Gheith Shereen M. F. , Gocke Christopher D.
Published: May 2020

The diffuse variant of follicular lymphoma (dFL) is a rare variant of FL lacking t(14;18) that was first described in 2009. In this study, we use a comprehensive approach to define unifying pathologic and genetic features through gold-standard pathologic review, FISH, SNP-microarray and next-generation sequencing of 16 cases of dFL. We found unique morphologic features, including interstitial sclerosis, microfollicle formation, and rounded nuclear cytology, confirmed absence of t(14;18) and recurrent deletion of 1p36, and showed a novel association with deletion/CN-LOH of 16p13 (inclusive ofCREBBP, CIITAandSOCS1). Mutational profiling demonstrated near-uniform mutations inCREBBPandSTAT6, with clonal dominance ofCREBBP, among other mutations typical of germinal-center B-cell lymphomas. FrequentCREBBPandCIITAco-deletion/mutation suggested a mechanism for immune evasion, while subclonalSTAT6activating mutations with concurrentSOCS1loss suggested a mechanism of BCL-xL/BCL2L1 upregulation in the absence ofBCL2rearrangements. A review of the literature showed significant enrichment for 16p13 and 1p36 loss/CN-LOH,STAT6mutation, andCREBBPandSTAT6co-mutation in dFL, as compared to conventional FL. With this comprehensive approach, our study demonstrates confirmatory and novel genetic associations that can aid in the diagnosis and subclassification of this rare type of lymphoma.
Correction for both common and rare cell types in blood is important to identify genes that correlate with age
Authors: Pellegrino Coppola Damiano , Claringbould Annique , Stutvoet Maartje ,   BIOS Consortium, Boomsma Dorret I. , Ikram M. Arfan , Slagboom Eline , Westra Harm-Jan , Franke Lude
Published: May 2020

Background

Aging is a multifactorial process that affects multiple tissues and is characterized by changes in homeostasis over time, leading to increased morbidity. Whole blood gene expression signatures have been associated with aging and have been used to gain information on its biological mechanisms, which are still not fully understood. However, blood is composed of many cell types whose proportions in blood vary with age. As a result, previously observed associations between gene expression levels and aging might be driven by cell type composition rather than intracellular aging mechanisms. To overcome this, previous aging studies already accounted for major cell types, but the possibility that the reported associations are false positives driven by less prevalent cell subtypes remains.

Results

Here, we compared the regression model from our previous work to an extended model that corrects for 33 additional white blood cell subtypes. Both models were applied to whole blood gene expression data from 3165 individuals belonging to the general population (age range of 18-81 years). We evaluated that the new model is a better fit for the data and it identified fewer genes associated with aging (625, compared to the 2808 of the initial model; P ≤ 2.5 × 10−6). Moreover, 511 genes (∼18% of the 2,808 genes identified by the initial model) were found using both models, indicating that the other previously reported genes could be proxies for less abundant cell types. In particular, functional enrichment of the genes identified by the new model highlighted pathways and GO terms specifically associated with platelet activity.

Conclusions

We conclude that gene expression analyses in blood strongly benefit from correction for both common and rare blood cell types, and recommend using blood-cell count estimates as standard covariates when studying whole blood gene expression.