bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface pressure impact on nitrogen-dominated USP super-Earth atmospheres
Authors: Chouqar J , Lustig-Yaeger J , Benkhaldoun Z , Szentgyorgyi A , Jabiri A , Soubkiou A
Published: April 2023

In this paper, we compare the chemistry and the emission spectra of nitrogen-dominated cool, warm, and hot ultra-short-period (USP) super-Earth atmospheres in and out of chemical equilibrium at various surface pressure scenarios ranging from 10−1 to 10 bar. We link the one-dimensional vulcan chemical kinetic code, in which thermochemical kinetic and vertical transport and photochemistry are taken into account, to the one-dimensional radiative transfer model, petitradtrans, to predict the emission spectra of these planets. The radiative–convective temperature–pressure profiles were computed with the helios code. Then, using pandexo noise simulator, we explore the observability of the differences produced by disequilibrium processes with the JWST. Our grids show how different surface pressures can significantly affect the temperature profiles, the atmospheric abundances, and consequently the emission spectra of these planets. We find that the divergences due to disequilibrium processes would be possible to observe in cooler planets by targeting HCN, C2H4, and CO, and in warmer planets by targeting CH4 with HCN, using the NIRSpec and MIRI LRS JWST instruments. These species are also found to be sensitive indicators of the existence of surfaces on nitrogen-dominated USP super-Earths, providing information regarding the thickness of these atmospheres.
Multiple stellar populations in globular clusters with JWST: an NIRCam view of 47 Tucanae
Authors: Milone A P , Marino A F , Dotter A , Ziliotto T , Dondoglio E , Cordoni G , Jang S , Lagioia E P , Legnardi M V , Mohandasan A , Tailo M , Yong D , Baimukhametova S , Carlos M
Published: April 2023

We use images collected with the near-infrared camera (NIRCam) onboard the JWST and with the Hubble Space Telescope (HST) to investigate multiple populations at the bottom of the main sequence (MS) of 47 Tucanae. The mF115W versus mF115W − mF322W2 colour–magnitude diagram (CMD) from NIRCam shows that, below the knee, the MS stars span a wide colour range, where the majority of M-dwarfs exhibit blue colours, and a tail of stars are distributed towards the red. A similar pattern is observed from the mF160W versus mF110W − mF160W CMD from HST, and multiple populations of M-dwarfs are also visible in the optical mF606W versus mF606W − mF814W CMD. The NIRCam CMD shows a narrow sequence of faint MS stars with masses smaller than $0.1\, \mathcal {M}_{\odot }$. We introduce a chromosome map of M-dwarfs that reveals an extended first population and three main groups of second-population stars. By combining isochrones and synthetic spectra with appropriate chemical composition, we simulate colours and magnitudes of different stellar populations in the NIRCam filters (at metallicities [Fe/H] = −1.5 and [Fe/H] = −0.75) and identify the photometric bands that provide the most efficient diagrams to investigate the multiple populations in globular clusters. Models are compared with the observed CMDs of 47 Tucanae to constrain M-dwarfs’ chemical composition. Our analysis suggests that the oxygen range needed to reproduce the colours of first- and second-population M-dwarfs is similar to that inferred from spectroscopy of red giants, constraining the proposal that the chemical variations are due to mass transfer phenomena in proto-clusters.
Spectral and temporal studies of Swift  J1658.2–4242 using AstroSat observations with the JeTCAF model
Authors: Mondal Santanu , Jithesh V
Published: April 2023

We present the X-ray spectral and temporal analysis of the black hole X-ray transient Swift  J1658.2–4242 observed by AstroSat. Three epochs of data have been analysed using the JeTCAF model to estimate the mass accretion rates and to understand the geometry of the flow. The best-fitting disc mass accretion rate ($\dot{m}_{\rm d}$) varies between $0.90^{+0.02}_{-0.01}$ and $1.09^{+0.04}_{-0.03}$$\dot{M}_{\rm Edd}$ in these observations, while the halo mass accretion rate changes from $0.15^{+0.01}_{-0.01}$ to $0.25^{+0.02}_{-0.01}$$\dot{M}_{\rm Edd}$. We estimate the size of the dynamic corona that varies substantially from $64.9^{+3.9}_{-3.1}$ to $34.5^{+2.0}_{-1.5}$ rg and a moderately high jet/outflow collimation factor stipulates isotropic outflow. The inferred high disc mass accretion rate and bigger corona size indicate that the source might be in the intermediate to soft spectral state of black hole X-ray binaries. The mass of the black hole estimated from different model combinations is ∼14 M⊙. In addition, we compute the quasi-periodic oscillation (QPO) frequencies from the model-fitted parameters, which match the observed QPOs. We further calculate the binary parameters of the system from the decay profile of the light curve and the spectral parameters. The estimated orbital period of the system is 4.0 ± 0.4 h by assuming the companion as a mid or late K-type star. Our analysis using the JeTCAF model sheds light on the physical origin of the spectrotemporal behaviour of the source, and the observed properties are mainly due to the change in both the mass accretion rates and absorbing column density.
Meiotic Recognition of Evolutionarily Diverged Homologs: Chromosomal Hybrid Sterility Revisited
Authors: Forejt Jiri , Jansa Petr
Published: April 2023

Hybrid sterility (HS) is an early postzygotic reproductive isolation mechanism observed in all sexually reproducing species. Infertility of hybrids prevents gene flow between incipient species and leads to speciation. While Drosophila studies have focused almost exclusively on the genic control of HS, two other model species, Mus musculus and budding yeast, provided the first experimental evidence of hybrid sterility governed by the nongenic effects of DNA sequence divergence. Here, we propose that the nongenic effect of increasing DNA divergence between closely related species may impair mutual recognition of homologous chromosomes and disrupt their synapsis. Unsynapsed or mispaired homologs can induce early meiotic arrest, or their random segregation can cause aneuploidy of spermatids and sperm cells. Impaired recognition of homologs may thus act as a universal chromosomal checkpoint contributing to the complexity of genetic control of HS. Chromosomal HS controlled by the Prdm9 gene in mice and HS driven by the mismatch repair machinery in yeast are currently the most advanced examples of chromosomal homology search-based HS. More focus on the cellular and molecular phenotypes of meiosis will be needed to further validate the role of homolog recognition in hybrid sterility and speciation.
Multicolor and multi-spot observations of Starlink’s Visorsat
Authors: Horiuchi Takashi , Hanayama Hidekazu , Ohishi Masatoshi , Nakaoka Tatsuya , Imazawa Ryo , Kawabata Koji S , Takahashi Jun , Onozato Hiroki , Saito Tomoki , Yamanaka Masayuki , Nogami Daisaku , Tampo Yusuke , Kojiguchi Naoto , Ito Jumpei , Shibata Masaaki , Schramm Malte , Oasa Yumiko , Kanai Takahiro , Oide Kohei , Murata Katsuhiro L , Hosokawa Ryohei , Takamatsu Yutaka , Imai Yuri , Ito Naohiro , Niwano Masafumi , Takagi Seiko , Ono Tatsuharu , Kouprianov Vladimir V
Published: April 2023

This study provides the results of simultaneous multicolor observations for the first Visorsat (STARLINK-1436) and the ordinary Starlink satellite (STARLINK-1113) in the U, B, V, g′, r, i, RC, IC, $z$, J, H, and Ks bands to quantitatively investigate the extent to which Visorsat reduces its reflected light. Our results are as follows: (1) in most cases, Visorsat is fainter than STARLINK-1113, and the sunshade on Visorsat therefore contributes to the reduction of the reflected sunlight; (2) the magnitude at 550 km altitude (normalized magnitude) of both satellites often reaches the naked-eye limiting magnitude (<6.0); (3) from a blackbody radiation model of the reflected flux, the peak of the reflected components of both satellites is around the $z$ band; and (4) the albedo of the near-infrared range is larger than that of the optical range. Under the assumption that Visorsat and STARLINK-1113 have the same reflectivity, we estimate the covering factor, Cf, of the sunshade on Visorsat, using the blackbody radiation model: the covering factor ranges from 0.18 ≤ Cf ≤ 0.92. From the multivariable analysis of the solar phase angle (Sun–target–observer), the normalized magnitude, and the covering factor, the phase angle versus covering factor distribution presents a moderate anti-correlation between them, suggesting that the magnitudes of Visorsat depend not only on the phase angle but also on the orientation of the sunshade along our line of sight. However, the impact on astronomical observations from Visorsat-designed satellites remains serious. Thus, new countermeasures are necessary for the Starlink satellites to further reduce reflected sunlight.
From global climate goals to local practice—mission-oriented policy enactment in three Swedish regions
Authors: Brett Nancy , Magnusson Thomas , Andersson Hans
Published: April 2023

As the national and supranational levels of government embrace the concept of missions to solve wicked problems, the importance of understanding how missions move from one level of governance to another becomes essential. In this paper, we present a comparative case analysis of evolving regional biogas systems to consider how global missions on climate action are enacted in local practice. Referring to wickedness in terms of contestation, complexity, and uncertainty of both problems and solutions, we examine how such framings affect the operationalisation of the missions. Our results indicate that in the process of local translation, wickedness often increases, but additional wickedness does not always worsen the outcomes.
Caring Under Fire Across Three Continents: The Hadfield-Spears Ambulance, 1941–1945
Authors: Humbert Laure
Published: April 2023

During the Second World War, the Hadfield Spears ambulance took care of around 22,000 wounded and/or sick patients across three continents. This article analyses how military attacks and instances of violence impacted on the psychological, emotional and physical health of those attending the wounded within this mobile unit. While historiography of allied medicine develops apace, analysis of the Free French health service remains rare. Yet the history of the Hadfield Spears ambulance provides a fascinating window into the neglected issue of attacks on healthcare in wartime, as well as a fresh scope for combining macro and micro perspectives. The deployment of both approaches suggests potent ways to connect intimate responses to attacks to broader histories of allied frictions and cooperation. Crucially, it offers rich insights into the development of a transnational ‘ethos of stoicism’, which helped to sustain the hospital’s community, in a fraught allied diplomatic context.
Does insomnia treatment prevent depression?
Authors: Boland Elaine M , Goldschmied Jennifer R , Gehrman Philip R
Published: April 2023

Rates of major depressive disorder (MDD) are increasing globally, in part due to the coronavirus disease 2019 pandemic, contributing to disease burden. It has long been known that insomnia is intricately connected with depression as indicated by greater depression severity and lower treatment response. Furthermore, insomnia is a significant risk factor for new-onset depression. Treatment of insomnia is thus a logical target for prevention of incidents and recurrent MDD. This systematic review sought to evaluate the current evidence for the preventive effects of insomnia treatment on depression onset. A database search yielded 186 studies, six of which met criteria for inclusion in this review. All of the studies utilized cognitive behavioral treatment for insomnia (CBT-I) as the target intervention and most delivered treatment via a digital platform. Four of the studies found significantly lower rates of MDD onset in those who received CBT-I compared to a control condition. The two remaining studies failed to confirm these effects in primary analyses but secondary analyses suggested evidence of a preventive effect. There was significant methodologic heterogeneity across studies in terms of sample selection, outcomes, and follow-up periods, limiting the ability to draw firm conclusions. The evidence overall is in the direction of insomnia treatment reducing the risk for onset of MDD, but further research is warranted.
Trustees’ duties: exemptions and exonerations
Authors: Hayton David
Published: April 2023

As part of the bargain for undertaking a trusteeship, a trustee can exempt itself not only from liability for a breach of trust, it can altogether oust particular trusteeship duties, so long as it leaves intact the irreducible core obligations of a trust. Where a trustee is to hold underlying controlled companies, the trustee’s duties of supervision and inquiry can be specifically ousted so long as the trustee has no actual or blind-eye knowledge of dishonest conduct in the affairs of such companies. Low insurance premiums lead to low trustees’ fees.
Weak set theories in foundational debates
Authors: Mathias A. R. D.
Published: April 2023

Perception of the relationship of the discipline of logic to other exact sciences changes with the years. No twentieth-century proposal for a single logical system that would support the whole of mathematics satisfied everyone, so weaker formal systems with applications in many different contexts are now sought, in mathematics, philosophy, computer science or elsewhere. As always, logicians help by asking such questions as ‘Is this theory correct for the given context?’ and ‘Can it be used in other contexts?’ The Introduction of this paper surveys the history of logic and its links to other scientific disciplines such as biology, economics, engineering and physics, and some details of current and future research projects are given. Then the very weak set theory
P
ROVI
is introduced and its support for the techniques of constructibility (Gödel 1935) and forcing (Cohen PJ 1963 The independence of the continuum hypothesis, I.
Proc. Natl Acad. Sci. USA
50
, 1143–1148. (
doi:10.1073/pnas.50.6.1143
)) is given in outline, full details being already in print. Relations with other known techniques are explored and developed. New results coming from the study of illfounded

ω

-models of
P
ROVI
and other systems are given; and new formal systems in the style of Quine (1937 Quine WV. 1936 Set-theoretic foundations for logic.
J. Symb. Log.
1
, 45–57. (
doi:10.2307/2268548
)) are described.

This article is part of the theme issue ‘Modern perspectives in Proof Theory’.
On the decomposition of WKL!!
Authors: Fujiwara Makoto , Nemoto Takako
Published: April 2023

From the conceptual viewpoint, many mathematical propositions implicitly contain at least two kinds of principle. One is a logical principle such as the law-of-excluded-middle or De Morgan’s law. Another is a function–existence principle. For both conceptual and practical reasons, it is an interesting enterprise to calibrate how amount of logical and function–existence principles are implicit in mathematical theorems and axioms. This is the topic of constructive reverse mathematics, which specifies necessary and sufficient axioms to prove each mathematical proposition constructively. In this paper, we decompose weak König’s lemma with a uniqueness hypothesis

WKL

!
!

by Moschovakis, into logical and function–existence principles in a recent framework of constructive reverse mathematics.

This article is part of the theme issue ‘Modern perspectives in Proof Theory’.
Classical consequences of constructive systems
Authors: Moschovakis Joan Rand
Published: April 2023

This is a survey of formal axiomatic systems for the three main varieties of constructive analysis, in a common language and with intuitionistic logic, which are as nearly as possible compatible with classical analysis and with one another. Classically sound consequences of principles of intuitionistic mathematics are emphasized. Compatibility with classical analysis is of two kinds. On the one hand, Bishop’s constructive mathematics and a very substantial part of intuitionistic analysis are classically correct, sharing with constructive recursive mathematics a neutral subsystem adequate for recursive function theory and elementary real analysis. On the other hand, each constructive system considered here is separately consistent with the negative interpretation of each of its classically sound subsystems, establishing internal compatibility with the classical context it is intended to refine. A possibly new criterion for the transposability of unique existential quantifiers and a recent theorem of Vafeiadou on the internal compatibility of classical and intuitionistic analysis are included.

This article is part of the theme issue ‘Modern perspectives in Proof Theory’.
Metric fixed point theory and partial impredicativity
Authors: Fernández-Duque D. , Shafer P. , Towsner H. , Yokoyama K.
Published: April 2023

We show that the Priess-Crampe & Ribenboim fixed point theorem is provable inRCA0. Furthermore, we show that Caristi’s fixed point theorem for both Baire and Borel functions is equivalent to the transfinite leftmost path principle, which falls strictly betweenATR0andΠ11-CA0. We also exhibit several weakenings of Caristi’s theorem that are equivalent toWKL0and toACA0.

This article is part of the theme issue ‘Modern perspectives in Proof Theory’.
The spectrum of Π31-soundness
Authors: Aguilera J. P. , Pakhomov F.
Published: April 2023

We study the

Π
3
1

-soundness spectra of theories. Given a recursively enumerable extension

T

of

A

C

A
0

,

O

3

1

(
T
)

is defined as the set of all 2-ptykes on which

T

is correct about well foundedness. This is a measure of how close

T

is to being

Π

3

1

-sound. We carry out a proof-theoretic classification of theories according to

O

3

1

(
T
)

, as well as a characterization of the sets of the form

O
3
1

(
T
)
∩

Δ
1
0

. Many of the results generalize to

n

greater than 3.

This article is part of the theme issue ‘Modern perspectives in Proof Theory’.
Some independence results related to finite trees
Authors: Friedman Harvey M. , Weiermann Andreas
Published: April 2023

We investigate some concrete independence results for systems of reverse mathematics which emerge from monotonicity properties of number-theoretic functions. Natural properties of the less than or equal to relation with respect to sums of natural numbers lead to independence results for first-order Peano arithmetic. Natural properties of the less than or equal to relation with respect to sums and products of natural numbers lead to independence results for arithmetical transfinite recursion. By considering number-theoretic functions of arbitrary arities, we obtain independence results for systems beyond arithmetical transfinite recursion. We discuss how these embeddability relations are related to tree embeddability relations and we consider variants where the tree embeddability relation is not assumed to preserve infima. The findings of this paper are complementary to results on Kruskal-like theorems proved earlier by the first author.

This article is part of the theme issue ‘Modern perspectives in Proof Theory’.
Ordinal analysis and the set existence property for intuitionistic set theories
Authors: Rathjen Michael
Published: April 2023

On account of being governed by constructive logic, intuitionistic theories

T

often enjoy various existence properties. The most common is the
numerical existence property
(NEP). It entails that an existential theorem of

T

of the form

(
∃
x
∈

N

)
A
(
x
)

can be witnessed by a numeral

n
¯

such that

T

proves

A
(

n
¯

)

. While NEP holds almost universally for natural intuitionistic set theories, the general existence property (EP), i.e. the property of a theory that for every existential theorem, a provably definable witness can be found, is known to fail for some prominent intuitionistic set theories such as Intuitionistic Zermelo–Fraenkel set theory (IZF) and constructive Zermelo–Fraenkel set theory (CZF). Both of these theories are formalized with collection rather than replacement as the latter is often difficult to apply in an intuitionistic context because of the uniqueness requirement. In light of this, one is clearly tempted to single out collection as the culprit that stymies the EP in such theories. Beeson stated the following open problem:
‘Does any reasonable set theory with collection have the existence property?
and added in proof:
The problem is still open for IZF with only bounded separation
.’ (Beeson. 1985
Foundations of constructive mathematics
, p. 203. Berlin, Germany: Springer.) In this article, it is shown that IZF with bounded separation, that is, separation for formulas in which only bounded quantifiers of the forms

(
∀
x
∈
a
)
,
(
∃
x
∈
a
)
,
(
∀
x
⊆
a
)
,
(
∃
x
⊆
a
)

are allowed, indeed has the EP. Moreover, it is also shown that CZF with the exponentiation axiom in place of the subset collection axiom has the EP. Crucially, in both cases, the proof involves a detour through ordinal analyses of infinitary systems of intuitionistic set theory, i.e. advanced techniques from proof theory.

This article is part of the theme issue ‘Modern perspectives in Proof Theory’.
Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival
Authors: Simhal Anish K. , Maclachlan Kylee H. , Elkin Rena , Zhu Jiening , Norton Larry , Deasy Joseph O. , Oh Jung Hun , Usmani Saad Z. , Tannenbaum Allen
Published: April 2023

The plasma cell cancer multiple myeloma (MM) varies significantly in genomic characteristics, response to therapy, and long-term prognosis. To investigate global interactions in MM, we combined a known protein interaction network with a large clinically annotated MM dataset. We hypothesized that an unbiased network analysis method based on large-scale similarities in gene expression, copy number aberration, and protein interactions may provide novel biological insights. Applying a novel measure of network robustness, Ollivier-Ricci Curvature, we examined patterns in the RNA-Seq gene expression and CNA data and how they relate to clinical outcomes. Hierarchical clustering using ORC differentiated high-risk subtypes with low progression free survival. Differential gene expression analysis defined 118 genes with significantly aberrant expression. These genes, while not previously associated with MM, were associated with DNA repair, apoptosis, and the immune system. Univariate analysis identified 8/118 to be prognostic genes; all associated with the immune system. A network topology analysis identified both hub and bridge genes which connect known genes of biological significance of MM. Taken together, gene interaction network analysis in MM uses a novel method of global assessment to demonstrate complex immune dysregulation associated with shorter survival.

STATEMENT OF SIGNIFICANCE

Multiple myeloma has heterogenous clinical outcomes which are not well predicted by current prognostic scoring systems. Global assessment of gene-protein interactions using Ollivier-Ricci Curvature produces clusters of patients with defined prognostic significance, with high-risk groups harboring complex gene dysregulation impacting immune function.
A new tractable method for generating Human Alveolar Macrophage Like cells in vitro to study lung inflammatory processes and diseases
Authors: Pahari Susanta , Arnett Eusondia , Simper Jan , Azad Abul , Guerrero-Arguero Israel , Ye Chengjin , Zhang Hao , Cai Hong , Wang Yufeng , Lai Zhao , Jarvis Natalie , Lumbreras Miranda , Maselli-Caceres Diego Jose , Peters Jay , Torrelles Jordi B , Martinez-Sobrido Luis , Schlesinger Larry S
Published: April 2023

Alveolar macrophages (AMs) are unique lung resident cells that contact airborne pathogens and environmental particulates. The contribution of human AMs (HAM) to pulmonary diseases remains poorly understood due to difficulty in accessing them from human donors and their rapid phenotypic change duringin vitroculture. Thus, there remains an unmet need for cost-effective methods for generating and/or differentiating primary cells into a HAM phenotype, particularly important for translational and clinical studies. We developed cell culture conditions that mimic the lung alveolar environment in humans using lung lipids,i.e., Infasurf (calfactant, natural bovine surfactant) and lung-associated cytokines (GM-CSF, TGF-β, and IL-10) that facilitate the conversion of blood-obtained monocytes to an AM-Like (AML) phenotype and function in tissue culture. Similar to HAM, AML cells are particularly susceptible to bothMycobacterium tuberculosisand severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. This study reveals the importance of alveolar space components in the development and maintenance of HAM phenotype and function, and provides a readily accessible model to study HAM in infectious and inflammatory disease processes, as well as therapies and vaccines.

IMPORTANCE

Millions die annually from respiratory disorders. Lower respiratory track gas-exchanging alveoli maintain a precarious balance between fighting invaders and minimizing tissue damage. Key players herein are resident AMs. However, there are no easily accessiblein vitromodels of HAMs, presenting a huge scientific challenge. Here we present a novel model for generating AML cells based on differentiating blood monocytes in a defined lung component cocktail. This model is non-invasive, significantly less costly than performing a bronchoalveolar lavage, yields more AML cells than HAMs per donor and retains their phenotype in culture. We have applied this model to early studies ofM. tuberculosisand SARS-CoV-2. This model will significantly advance respiratory biology research.
Embryo-specific epigenetic mechanisms reconstitute the CHH methylation landscape during Arabidopsis embryogenesis
Authors: Hsieh Ping-Hung , Frost Jennifer M. , Choi Yeonhee , Hsieh Tzung-Fu , Zilberman Daniel , Fischer Robert L
Published: April 2023

The modification of flowering plant DNA by CHH methylation acts primarily to silence transposable elements, of which many active copies are present inArabidopsis thaliana. During embryogenesis, the CHH methylation landscape is dramatically reprogrammed, resulting in exceedingly high levels of this modification upon mature embryo formation. The mechanisms constituting the remodeling process, and its function in embryos, are unclear. Here, we isolate embryos from Arabidopsis plants harboring mutations for key components of the pathways that confer CHH methylation, namely RNA-directed DNA methylation (RdDM) and the Chromomethylase 2 (CMT2) pathways. We reveal that embryos are more methylated than leaves at shared CMT2 and RdDM targeting loci, accounting for most embryonic CHH hypermethylation. While the majority of embryo CHH methylated loci overlap with those in somatic tissues, a subset of conventional pericentric CMT2-methylated loci are instead targeted by RdDM in embryos. These loci, termed ‘embRdDM’ exhibit intermediate H3K9me2 levels, associated with increased chromatin accessibility. Strikingly, more than 50% of the embRdDM loci in pollen vegetative (nurse) cells andddm1mutant somatic tissues are also targeted by RdDM, and these tissues were also reported to exhibit increased chromatin accessibility in pericentric heterochromatin. Furthermore, the root columella stem cell niche also displays CHH hypermethylation and an enriched presence of small RNAs at embRdDM loci. Finally, we observe a significant overlap of CHH hypermethylated loci with endosperm DEMETER targeting sites, suggesting that non-cell autonomous communication within the seed may contribute to the epigenetic landscape of the embryo. However, similar overlap with vegetative cell DEMETER targets indicates that the chromatin landscape that allows DEMETER access is mirrored in developing embryos, permitting CHH methylation catalysis at the same loci. Our findings demonstrate that both conserved and embryo-specific epigenetic mechanisms reshape CHH methylation profiles in the dynamic chromatin environment of embryogenesis.
Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer
Authors: Lin Chin-Hsuan Sophie , Do Trang Thuy , Unsworth Lee , Garrido Marta I.
Published: April 2023

Numerous studies have found that the Bayesian framework, which formulates the optimal integration of the knowledge of the world (i.e. prior) and current sensory evidence (i.e. likelihood), captures human behaviours sufficiently well. However, there are debates regarding whether humans use precise but cognitively demanding Bayesian computations for behaviours. Across two studies, we trained participants to estimate hidden locations of a target drawn from priors with different levels of uncertainty. In each trial, scattered dots provided noisy likelihood information about the target location. Participants showed that they learned the priors and combined prior and likelihood information to infer target locations in a Bayes fashion. We then introduced a transfer condition presenting a trained prior and a likelihood that has never been put together during training. How well participants integrate this novel likelihood with their learned prior is an indicator of whether participants perform Bayesian computations. In one study, participants experienced the newly introduced likelihood, which was paired with a different prior, during training. Participants changed likelihood weighting following expected directions although the degrees of change were significantly lower than Bayes-optimal predictions. In another group, the novel likelihoods were never used during training. We found people integrated a new likelihood within (interpolation) better than the one outside (extrapolation) the range of their previous learning experience and they were quantitatively Bayes-suboptimal in both. We replicated the findings of both studies in a validation dataset. Our results showed that Bayesian behaviours may not always be achieved by a full Bayesian computation. Future studies can apply our approach to different tasks to enhance the understanding of decision-making mechanisms.

Author summary

Bayesian decision theory has emerged as a unified approach for capturing a wide range of behaviours under uncertainty. However, behavioural evidence supporting that humans use explicit Bayesian computation is scarce. While it has been argued that knowledge generalization should be treated as hard evidence of the use of Bayesian strategies, results from previous work were inconclusive. Here, we develop a marker that effectively quantifies how well humans transfer learned priors to a new scenario. Our marker can be applied to various tasks and thus can provide a path forwarding the understanding of psychological and biological underpinnings of inferential behaviours.
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products
Authors: Yu Tao , Luo Yingfeng , Tan Xinyu , Zhao Dahe , Bi Xiaochun , Li Chenji , Zheng Yanning , Xiang Hua , Hu Songnian
Published: April 2023

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. By analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiome. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes (MAGs), which represent 1897 species spanning 106 phyla. In addition, beta diversity analysis indicates that both sampling site and cold seep type have substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, indicating the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences encode potentially novel natural products. These natural products are dominated by ribosomal processing peptides, which are widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource which would enhance the understanding and utilization of global cold seep microbiomes.
Hunger- and thirst-sensing neurons modulate a neuroendocrine network to coordinate sugar and water ingestion
Authors: González-Segarra Amanda J. , Pontes Gina , Jourjine Nicholas , Toro Alexander Del , Scott Kristin
Published: April 2023

Consumption of food and water is tightly regulated by the nervous system to maintain internal nutrient homeostasis. Although generally considered independently, interactions between hunger and thirst drives are important to coordinate competing needs. InDrosophila, four neurons called the Interoceptive Subesophageal zone Neurons (ISNs) respond to intrinsic hunger and thirst signals to oppositely regulate sucrose and water ingestion. Here, we investigate the neural circuit downstream of the ISNs to examine how ingestion is regulated based on internal needs. Utilizing the recently available fly brain connectome, we find that the ISNs synapse with a novel cell type Bilateral T-shaped neuron (BiT) that projects to neuroendocrine centers.In vivoneural manipulations revealed that BiT oppositely regulates sugar and water ingestion. Neuroendocrine cells downstream of ISNs include several peptide-releasing and peptide-sensing neurons, including insulin producing cells (IPC), crustacean cardioactive peptide (CCAP) neurons, and CCHamide-2 receptor isoform RA (CCHa2R-RA) neurons. These neurons contribute differentially to ingestion of sugar and water, with IPCs and CCAP neurons oppositely regulating sugar and water ingestion, and CCHa2R-RA neurons modulating only water ingestion. Thus, the decision to consume sugar or water occurs via regulation of a broad peptidergic network that integrates internal signals of nutritional state to generate nutrient-specific ingestion.
Comparative analysis of noise-attenuation mechanisms in gene expression: From single cells to cell populations
Authors: Zhang Zhanhao , Nieto Cesar , Singh Abhyudai
Published: April 2023

Negative feedback regulation is a well-known motif for suppressing deleterious fluctuations in gene product levels. We systematically compare two scenarios where negative feedback is either implemented in the protein production rate (regulated synthesis) or in the protein degradation rate (regulated degradation). Our results show that while in lownoise regimes both schemes are identical, they begin to show remarkable differences in high-noise regimes. Analytically solving for the probability distributions of the protein levels reveals that regulated synthesis is a better strategy to suppress random fluctuations while also minimizing protein levels dipping below a threshold. In contrast, regulated degradation is preferred if the goal is to minimize protein levels going beyond a threshold. Finally, we compare and contrast these distributions not only in a single cell over time but also in an expanding cell population where these effects can be buffered or exacerbated due to the coupling between expression and cell growth.
Differential Expression of Gluconeogenesis-Related Transcripts in a Freshwater Zooplankton Model Organism Suggests a Role of the Cori Cycle in Hypoxia Tolerance
Authors: Malek M. C. , Behera J.R. , Kilaru A. , Yampolsky L. Y.
Published: April 2023

Gluconeogenesis (GNG) is the process of regenerating glucose and NAD+ that allows continuing ATP synthesis by glycolysis during fasting or in hypoxia. Recent data fromC. elegansand crustaceans challenged with hypoxia show differential and tissue-specific expression of GNG-specific genes.

Here we report differential expression of several GNG-specific genes in the head and body of a model organism,Daphnia magna,a planktonic crustacean, in normoxic and acute hypoxic conditions. We predict that GNG-specific transcripts will be enriched in the body, where most of the fat tissue is located, rather than in the head, where the tissues critical for survival in hypoxia, the central nervous system and locomotory muscles, are located. We measured the relative expression of GNG-specific transcripts in each body part by qRT-PCR and normalized them by either the expression of a reference gene or the rate-limiting glycolysis enzyme pyruvate kinase (PK).

Our data show that of the three GNG-specific transcripts tested, pyruvate carboxylase (PC) showed no differential expression in either the head or body. Phosphoenolpyruvate carboxykinase (PEPCK-C), on the other hand, is upregulated in hypoxia in both body parts. Fructose-1,6-bisphosphatase (FBP) is upregulated in the body relative to the head and upregulated in hypoxia relative to normoxia, with a stronger body effect in hypoxia when normalized by PK expression.

These results support our hypothesis thatDaphniacan survive hypoxic conditions by implementing the Cori cycle, where body tissues supply glucose and NAD+ to the brain and muscles, enabling them to continuously generate ATP by glycolysis.
The Ivory-billed Woodpecker: audio evidence and analyses from Southeast United States 2022
Authors: Williams John D.
Published: April 2023

The author has withdrawn the paper due to the changed wishes of the owner of the data. The owner disagrees with some of the conclusions reached and does not want the data called “2022 SE US 1,2,3,and 4” used in any form. If you have any questions, please contact the corresponding author.
Reply to Barton et al: signatures of natural selection during the Black Death
Authors: Vilgalys Tauras P. , Klunk Jennifer , Demeure Christian E. , Cheng Xiaoheng , Shiratori Mari , Madej Julien , Beau Rémi , Elli Derek , Patino Maria I. , Redfern Rebecca , DeWitte Sharon N. , Gamble Julia A. , Boldsen Jesper L. , Carmichael Ann , Varlik Nükhet , Eaton Katherine , Grenier Jean-Christophe , Golding G. Brian , Devault Alison , Rouillard Jean-Marie , Yotova Vania , Sindeaux Renata , Ye Chun Jimmie , Bikaran Matin , Dumaine Anne , Brinkworth Jessica F , Missiakas Dominique , Rouleau Guy A. , Steinrücken Matthias , Pizarro-Cerdá Javier , Poinar Hendrik N. , Barreiro Luis B.
Published: April 2023

Bartonet al.1raise several statistical concerns regarding our original analyses2that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high FSTvalues at the immune loci relative to putatively neutral sites after switching the allele frequency estimation method to a maximum likelihood approach, filtering to only consider known human variants, and down-sampling our data to the same mean coverage across sites. Furthermore, using permutations, we show that the rs2549794 variant nearERAP2continues to emerge as the strongest candidate for selection (p = 1.2×10−5), falling below the Bonferroni-corrected significance threshold recommended by Bartonet al. Importantly, the evidence for selection onERAP2is further supported by functional data demonstrating the impact of theERAP2genotype on the immune response toY. pestisand by epidemiological data from an independent group showing that the putatively selected allele during the Black Death protects against severe respiratory infection in contemporary populations.
Determining the Statistical Significance of the Difference Between Arbitrary Curves: A Spreadsheet Method
Authors: Hristova Kalina , Wimley William C.
Published: April 2023

We present a simple, spreadsheet-based method to determine the statistical significance of the difference between any two arbitrary curves. This modified Chi-squared method addresses two scenarios: A single measurement at each point with known standard deviation, or multiple measurements at each point averaged to produce a mean and standard error. The method includes an essential correction for the deviation from normality in measurements with small sample size, which are typical in biomedical sciences. Statistical significance is determined without regard to the functionality of the curves, or the signs of the differences. Numerical simulations are used to validate the procedure. Example experimental data are used to demonstrate its application. An Excel spreadsheet is provided for performing the calculations for either scenario.
Insulin-like peptides regulate oogenesis by stimulating ovarian ecdysteroid production in the Indian malaria mosquitoAnopheles stephensi
Authors: Phipps Benjamin L. , Brown Mark R. , Strand Michael R.
Published: April 2023

Females of many mosquito species feed on vertebrate blood to produce eggs, making them effective disease vectors. In the dengue vectorAedes aegypti, blood feeding signals the brain to release ovary ecdysteroidogenic hormone (OEH) and insulin-like peptides (ILPs) that trigger ecdysteroid production by the ovaries. These ecdysteroids regulate synthesis of the yolk protein vitellogenin (Vg) that is packaged into eggs. Less is known about the reproductive biology ofAnophelesmosquitoes, which pose a greater public health threat thanAedesspp. because they are competent to transmit mammalian malaria. ILPs can triggerAn. stephensiovaries to secrete ecdysteroids. UnlikeAe. aegypti,Anophelesalso transfer ecdysteroids fromAnophelesmales to females during mating. To elucidate the role of OEH and ILPs inAn. stephensi, we decapitated blood-fed females to ablate the source of these peptides and injected them with each hormone. Yolk deposition into oocytes was abolished in decapitated females and rescued by ILP injection. ILP activity was dependent on blood feeding and little change in triglyceride and glycogen stores was observed in response to blood-feeding, suggesting this species requires nutrients from blood to form eggs. We also measured egg maturation, ecdysteroid titers, and yolk protein expression in mated and virgin females. Although yolk deposition into developing oocytes was significantly reduced in virgins compared to mated females, no differences in ecdysteroid titers or Vg transcript abundance were detected between these groups. 20-hydroxyecdysone (20E) stimulated Vg expression in female fat bodies in primary culture. Given these results, we conclude that ILPs control egg formation by regulating ecdysteroid production in the ovaries.
Shifts in the coral microbiome in response toin situexperimental deoxygenation
Authors: Howard Rachel D. , Schul Monica , Rodriguez Bravo Lucia M. , Altieri Andrew , Meyer Julie L.
Published: April 2023

Global climate change impacts ocean communities through rising surface temperatures, ocean acidification, and deoxygenation. While the response of the coral holobiont to the first two effects has been relatively well studied, little is known about the response of the coral microbiome to deoxygenation. In this study, we investigated the response of the microbiome to hypoxia in two coral species that differ in their relative tolerance to hypoxia. We conductedin situoxygen manipulations on a coral reef in Bahía Almirante, Panama, which has previously experienced episodes of low dissolved oxygen concentrations. Naïve coral colonies (previously unexposed to hypoxia) of massive starlet coral (Siderastrea siderea) and Lamarck’s sheet coral (Agaricia lamarcki) were transplanted to a reef and either enclosed in chambers that created hypoxic conditions or left at ambient oxygen levels. We collected samples of surface mucus and tissue after 48 hours of exposure and characterized the microbiome by sequencing 16S rRNA genes. We found that the microbiomes of the two coral species were distinct from one another and remained so after exhibiting similar shifts in microbiome composition in response to hypoxia. There was an increase in both abundance and number of taxa of anaerobic microbes after exposure to hypoxia. Some of these taxa may play beneficial roles in the coral holobiont by detoxifying the surrounding environment during hypoxic stress. This work describes the first characterization of the coral microbiome under hypoxia and is an initial step toward identifying potential beneficial bacteria for corals facing this environmental stressor.

Importance

Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Deoxygenation on coral reefs will worsen with ongoing climate change, acidification, and eutrophication. We do not yet understand the response of the coral microbiome to hypoxia, and whether this reaction may have a beneficial or harmful role in the coral holobiont. To understand how the coral microbial community structure responds during hypoxic stress, we experimentally lowered the oxygen levels around corals in the field to observe changes in the composition of the coral microbiome. We documented the increase of anaerobic and pathogenic bacteria in the microbiomes of the massive starlet coral (Siderastrea siderea) and Lamarck’s sheet coral (Agaricia lamarcki) in 48 hours. This work provides fundamental knowledge of the microbial response in the coral holobiont during hypoxia and may provide insight to holobiont function during stress.
Insight into the genetic diversity, resistance, and virulence ofListeriafrom the marine environment: reveal the risk of hypervirulent isolates
Authors: Pan Mao , Yan Wang , Lingling Li , Shunshi Ji , Peijing Li , Lingyun Liu , Jinni Chen , Hui Sun , Xia Luo , Changyun Ye
Published: April 2023

Listeria monocytogenes is a major human foodborne pathogen and a ubiquitous environmental saprophyte. In this study, we investigated the prevalence and characteristics ofListeria spp. from beach sand in the coastal environment. Three differentListeria spp.,Listeria monocytogenes(n=16),Listeria fleishmanii(n=7), andListeria aquatica(n=3) were isolated from 769 beach sand samples and demonstrated diverse biofilm forming capacity. TheL. monocytogenesisolates belonged to four distinct sequence types (ST87, ST121, ST35, and ST85) and contained the majority of virulence genes, some isolates were hypervirulent clones or had close phylogenetic relatedness with clinical cases. The ST87 isolates showed higher ability of biofilm formation in seawater than other STs strains. As a reservoir of microbes from marine environments and human/animal excrement, coastal sand would play an important role in the spread ofL. monocytogenes and is an environmental risk for human listeriosis.