bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of the caudal peduncle in a fish-inspired robotic model: how changing stiffness and angle of attack affects swimming performance
Authors: Matthews David G , Zhu Ruijie , Wang Junshi , Dong Haibo , Bart-Smith Hilary , Lauder George
Published: October 2022

In fish, the tail is a key element of propulsive anatomy that contributes to thrust during swimming. Fish possess the ability to alter tail stiffness, surface area and conformation. Specifically, the region at the base of the tail, the caudal peduncle, is proposed to be a key location of fish stiffness modulation during locomotion. Most previous analyses have focused on the overall body or tail stiffness, and not on the effects of changing stiffness specifically at the base of the tail in fish and robotic models. We used both computational fluid dynamics analysis and experimental measurements of propulsive forces in physical models with different peduncle stiffnesses to analyze the effect of altering stiffness on the tail angle of attack and propulsive force and efficiency. By changing the motion program input to the tail, we were able to alter the phase relationship between the front and back tail sections between 0° and 330°. Computational simulations showed that power consumption was nearly minimized and thrust production was nearly maximized at the kinematic pattern where φ = 270°, the approximate phase lag observed in the experimental foils and in free swimming tuna. We observed reduced thrust and efficiency at high angles of attack, suggesting that the tail driven during these motion programs experiences stalling and loss of lift. However, there is no single peduncle stiffness that consistently maximizes performance, particularly in physical models. This result highlights the fact that the optimal caudal peduncle stiffness is highly context dependent. Therefore, incorporating the ability to control peduncle stiffness in future robotic models of fish propulsion promises to increase the ability of robots to approach the performance of fish.
Adaptive approaches to REDD+ are needed for countries with high forest cover and low deforestation rates
Authors: Schweikart Melanie , Mertz Ole , Müller Daniel
Published: October 2022

Reducing emissions from deforestation and forest degradation (REDD+) aims to maintain forest carbon stocks above benchmark reference levels through financial compensation. However, countries with high forest cover and low deforestation (HFLD) are unlikely to be compensated fairly if REDD+ initiatives fail to conserve existing forests and to incentivize low deforestation rates. Here we analyze the submissions of forest reference levels (FRLs) of five HFLD countries [Democratic Republic of the Congo (DRC), Republic of the Congo (Congo), Guyana, Papua New Guinea, Suriname] to the REDD+ platform of the United Nations Framework Convention on Climate Change. We assessed if the FRLs are likely to yield compensation payments that maintain carbon stocks above the business-as-usual scenario and compared the FRLs with quantitative emission data. Our results show that only Guyana submitted an FRL that yielded sufficient monetary incentives for low deforestation rates. Compensation payments will likely be insufficient in Suriname, Papua New Guinea, and the Congo. The FRL of the DRC would generate the highest compensation payment (on average US$ 1.3 billion annually). Overall, our results suggest that payments from REDD+ will fail to provide adequate incentives for most HFLD countries. We suggest that the FRL should allow for post hoc adaptation to changes in the drivers of deforestation. This implies that REDD+ schemes need sufficient flexibility to reflect changes in the opportunity costs of alternative land uses, which is particularly acute for HFLD countries where pressure on forests can accumulate rapidly. More adaptive REDD+ likely better rewards HFLD countries in ways that preserve their valuable forest ecosystems.
Symmetry operators of the asymmetric two-photon quantum Rabi model
Authors: Xie You-Fei , Chen Qing-Hu
Published: October 2022

The true level crossings in a subspace of the asymmetric two-photon quantum Rabi model (tpQRM) have been observed when the bias parameter of qubit is an even multiple of the renormalized cavity frequency. Generally, such level crossings imply the existence of the hidden symmetry because the bias term breaks the obvious symmetry exactly. In this work, we propose a Bogoliubov operator approach for the asymmetric tpQRM to derive the symmetry operators associated with the hidden symmetry hierarchically. The explicit symmetry operators consisting of Lie algebra at low biases can be easily obtained in our general scheme. We believe the present approach can be extended for other asymmetric Rabi models to find the relevant hidden symmetry.
CT organ dose calculator size adaptive for pediatric and adult patients
Authors: Lee Choonsik , Yeom Yeon Soo , Folio Les
Published: October 2022

Background. Although computed tomography (CT) has played a critical role in medical care since its introduction in the 1970s, its potential long-term risk of adverse health effects has been of concern. It is crucial to accurately estimate the radiation dose delivered to the patient’s critical organs to ensure the dose is As Low As Reasonably Achievable. However, organ-level dose calculation tools for pediatric and adult patients with various body sizes are rare. We extended the existing CT organ dose calculator, NCICT 1.0, which is based on reference-size phantoms, to include body size-specific pediatric and adult phantoms. Methods. We calculated body size-specific organ doses normalized to CTDIvol by using a library of 158 pediatric and 193 adult computational human phantoms with various body sizes combined with a Monte Carlo radiation transport code, MCNP6. We also created a library of generic tube current modulation (TCM) profiles for the phantom library using a ray-tracing algorithm and implemented them into organ dose calculations. We validated organ doses for the body size-specific phantoms using those calculated from ten abdominal CT patients. We also evaluated potential dosimetric errors caused by only using reference phantoms for patients with different body sizes. Results. Organ dose coefficients and TCM profiles for 351 pediatric and adult body size-specific phantoms were implemented into NCICT 2.0. The dose coefficients from the ten abdominal CT patients agreed with those from the program within 13%. The organ doses for the overweight phantoms were overestimated by over 80% when only reference size phantoms were used. Conclusion. We confirmed that the upgraded dose calculator NCICT 2.0 could substantially reduce potential dosimetric errors caused by using only reference size phantoms. The program should be useful for the radiology community to accurately monitor organ doses for pediatric and adult CT patients with various body sizes.
Ultrabright and narrowband intra-fiber biphoton source at ultralow pump power
Authors: Bruns Alexander , Hsu Chia-Yu , Stryzhenko Sergiy , Giese Enno , Yatsenko Leonid P , Yu Ite A , Halfmann Thomas , Peters Thorsten
Published: October 2022

Nonclassical photon sources of high brightness are key components of quantum communication technologies. We here demonstrate the generation of narrowband, nonclassical photon pairs by employing spontaneous four-wave mixing in an optically-dense ensemble of cold atoms within a hollow-core fiber. The brightness of our source approaches the limit of achievable generated spectral brightness at which successive photon pairs start to overlap in time. For a generated spectral brightness per pump power of up to 2 × 109 pairs/(s MHz mW) we observe nonclassical correlations at pump powers below 100 nW and a narrow bandwidth of 2π × 6.5 MHz. In this regime we demonstrate that our source can be used as a heralded single-photon source. By further increasing the brightness we enter the regime where successive photon pairs start to overlap in time and the cross-correlation approaches a limit corresponding to thermal statistics. Our approach of combining the advantages of atomic ensembles and waveguide environments is an important step toward photonic quantum networks of ensemble-based elements.
Improving optical properties of wurtzite GaN with C and Fe co-doping: A DFT+U study
Authors: Zaman Akib , Mumu Homayra Tabassum , Aunkon Rafat Hossain , Bhuiyan Faharia Hasan , Sharif Ahmed
Published: October 2022

Density Functional Theory with Hubbard U parameter (DFT + U) was used to study the impact of C (6.25%) and Fe (12.5%) mono- and co-doping on wurtzite GaN, which modified the structural, electrical, magnetic, and optical properties. Under conditions of abundant N, the doping effect led to an increase in thermodynamic formability. For all the dopant combinations, a reduction in the band gap was seen. GaN becomes a ferrimagnetic material because of co-doping. The performance of the C and Fe co-doped GaN was the best due to the redshift of the absorption edge, which resulted in the improved absorption of near ultraviolet (UV) and visible-infrared (VIS-IR) photonic energies for both monodoping and co-doping structures. The doping caused an increase in the refractive index and dielectric constant. For C and Fe co-doped GaN, the maximum static dielectric constant and refractive index were 19.58 and 4.45, respectively. The findings of this work therefore point to the possible use of C, Fe mono- and co-doped GaN in UV, IR optoelectronic and photonic devices.
Analysis of mechanical and thermal properties of polypropylene composite reinforced with Luffa cylindrica
Authors: de Souza Campos Rafael , Furtado de Sousa Ana Maria , Zawadzki Sônia Faria , Corrêa Harrison Lourenço
Published: October 2022

Vegetable fibers have an economic potential to be employed as polymer reinforcement. This is due to their low cost, biodegradability, recyclability, adequate mechanical properties, and because they come from renewable sources. The growing need for alternative materials that meet the demands of various industrial segments (aerospace, mechanics, automobile, petrochemistry, shipping, civil engineering etc) requires detailed investigations on their physical, mechanical, and chemical properties. Detailed information about the behavior of fibers in a polymer matrix can indicate whether they can produce a structural composite. This work investigated the mechanical and thermal properties of polypropylene (PP) samples containing 0%, 10%, and 20% (w/w) Luffa cylindrica fibers, as well as to analyze the morphology of the fibers before and after their processing with the polymer. The mechanical results of the composites showed that those plant fibers reduced the strain of pure PP, increasing its stiffness. Thermogravimetric trials revealed that the composite had its thermal stability reduced with an increase in fiber content.
A Probabilistic Approach to Classical Solutions of the Master Equation for Large Population Equilibria
Authors: Chassagneux Jean-François , Crisan Dan , Delarue François
Published: October 2022

We analyze a class of nonlinear partial differential equations (PDEs) defined on

R

d

×

P

2

(

R

d

)
,

\mathbb {R}^d \times \mathcal {P}_2(\mathbb {R}^d),

where

P

2

(

R

d

)

\mathcal {P}_2(\mathbb {R}^d)

is the Wasserstein space of probability measures on

R

d

\mathbb {R}^d

with a finite second-order moment. We show that such equations admit a classical solutions for sufficiently small time intervals. Under additional constraints, we prove that their solution can be extended to arbitrary large intervals. These nonlinear PDEs arise in the recent developments in the theory of large population stochastic control. More precisely they are the so-called master equations corresponding to asymptotic equilibria for a large population of controlled players with mean-field interaction and subject to minimization constraints. The results in the paper are deduced by exploiting this connection. In particular, we study the differentiability with respect to the initial condition of the flow generated by a forward-backward stochastic system of McKean-Vlasov type. As a byproduct, we prove that the decoupling field generated by the forward-backward system is a classical solution of the corresponding master equation. Finally, we give several applications to mean-field games and to the control of McKean-Vlasov diffusion processes.
Adiabatic Evolution and Shape Resonances
Authors: Hitrik Michael , Mantile Andrea , Sjoestrand Johannes
Published: October 2022

Motivated by a problem of one mode approximation for a non-linear evolution with charge accumulation in potential wells, we consider a general linear adiabatic evolution problem for a semi-classical Schrödinger operator with a time dependent potential with a well in an island. In particular, we show that we can choose the adiabatic parameter

ε
\varepsilon

with

ln
⁡
ε
≍
−
1

/

h

\ln \varepsilon \asymp -1/h

, where

h
h

denotes the semi-classical parameter, and get adiabatic approximations of exact solutions over a time interval of length

ε

−
N

\varepsilon ^{-N}

with an error

O

(

ε
N

)

{\mathcal O}(\varepsilon ^N)

. Here

N
>
0

N>0

is arbitrary.

\center Résumé \endcenter

Motivés par un problème d’approximation à un mode pour une évolution avec accumulation de charge dans des puits de potentiel, nous considérons un problème d’évolution linéaire pour un opérateur de Schrödinger avec un potentiel dépendant du temps avec un puits dans une île. En particular, nous montrons que nous pouvons choisir le paramètre adiabatique

ε
\varepsilon

avec

ln
⁡
ε
≍
−
1

/

h

\ln \varepsilon \asymp -1/h

, où

h
h

désigne le paramètre semi-classique, et obtenir des approximations adiabatiques de solutions exactes sur des intervalles de temps de longueur

ε

−
N

\varepsilon ^{-N}

avec une erreur

O

(

ε
N

)

{\mathcal O}(\varepsilon ^N)

. Ici

N
>
0

N>0

est arbitraire.
Asymptotic Spreading for General Heterogeneous Fisher-KPP Type Equations
Authors: Berestycki Henri , Nadin Grégoire
Published: October 2022

In this monograph, we review the theory and establish new and general results regarding spreading properties for heterogeneous reaction-diffusion equations:
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="partial-differential Subscript t Baseline u minus sigma-summation Underscript i comma j equals 1 Overscript upper N Endscripts a Subscript i comma j Baseline left-parenthesis t comma x right-parenthesis partial-differential Subscript i j Baseline u minus sigma-summation Underscript i equals 1 Overscript upper N Endscripts q Subscript i Baseline left-parenthesis t comma x right-parenthesis partial-differential Subscript i Baseline u equals f left-parenthesis t comma x comma u right-parenthesis period">

∂

t

u
−

∑

i
,
j
=
1

N

a

i
,
j

(
t
,
x
)

∂

i
j

u
−

∑

i
=
1

N

q
i

(
t
,
x
)

∂
i

u
=
f
(
t
,
x
,
u
)
.

\begin{equation*} \partial _{t} u - \sum _{i,j=1}^N a_{i,j}(t,x)\partial _{ij}u-\sum _{i=1}^N q_i(t,x)\partial _i u=f(t,x,u). \end{equation*}

These are concerned with the dynamics of the solution starting from initial data with compact support. The nonlinearity

f
f

is of Fisher-KPP type, and admits

0
0

as an unstable steady state and

1
1

as a globally attractive one (or, more generally, admits entire solutions

p
±

(
t
,
x
)

p^\pm (t,x)

, where

p
−

p^-

is unstable and

p
+

p^+

is globally attractive). Here, the coefficients

a

i
,
j

,

q
i

,
f

a_{i,j}, q_i, f

are only assumed to be uniformly elliptic, continuous and bounded in

(
t
,
x
)

(t,x)

. To describe the spreading dynamics, we construct two non-empty star-shaped compact sets

S

_

⊂

S

¯

⊂

R

N

\underline {\mathcal {S}}\subset \overline {\mathcal {S}} \subset \mathbb {R}^N

such that for all compact set

K
⊂

i
n
t

(

S

_

)

K\subset \mathrm {int}(\underline {\mathcal {S}})

(resp. all closed set

F
⊂

R

N

∖

S

¯

F\subset \mathbb {R}^N\backslash \overline {\mathcal {S}}

), one has

lim

t
→
+
∞

sup

x
∈
t
K

|

u
(
t
,
x
)
−
1

|

=
0

\lim _{t\to +\infty } \sup _{x\in tK} |u(t,x)-1| = 0

(resp.

lim

t
→
+
∞

sup

x
∈
t
F

|

u
(
t
,
x
)

|

=
0

\lim _{t\to +\infty } \sup _{x\in tF} |u(t,x)| =0

).

The characterizations of these sets involve two new notions of generalized principal eigenvalues for linear parabolic operators in unbounded domains. In particular, it allows us to show that

S

¯

=

S

_

\overline {\mathcal {S}}=\underline {\mathcal {S}}

and to establish an exact asymptotic speed of propagation in various frameworks. These include: almost periodic, asymptotically almost periodic, uniquely ergodic, slowly varying, radially periodic and random stationary ergodic equations. In dimension

N
N

, if the coefficients converge in radial segments, again we show that

S

¯

=

S

_

\overline {\mathcal {S}}=\underline {\mathcal {S}}

and this set is characterized using some geometric optics minimization problem. Lastly, we construct an explicit example of non-convex expansion sets.
Partial Compactification of Monopoles and Metric Asymptotics
Authors: Kottke Chris , Singer Michael
Published: October 2022

We construct a partial compactification of the moduli space,

M

k

\mathcal {M}_k

, of

S
U

(
2
)

\mathrm {SU}(2)

magnetic monopoles on

R

3

\mathbb {R}^3

, wherein monopoles of charge

k
k

decompose into widely separated ‘monopole clusters’ of lower charge going off to infinity at comparable rates. The hyperKähler metric on

M

k

\mathcal {M}_k

has a complete asymptotic expansion up to the boundary, the leading term of which generalizes the asymptotic metric discovered by Bielawski, Gibbons and Manton when each lower charge is 1.
Mackey Profunctors
Authors: Kaledin D.
Published: October 2022

In the standard theory of Mackey functors for a group

G
G

, the group is either finite, or a compact Lie group. In the present paper, we develop an alternative notion of a Mackey profunctor that works better for profinite groups. The most important practical example is

G
=

Z

^

G=\widehat {\mathbb {Z}}

, the profinite completion of the group of the integers, and in this case, our Mackey profunctors appear naturally in the theory of cyclotomic traces.
Adrenal Ablation Versus Mineralocorticoid Receptor Antagonism for the Treatment of Primary Aldosteronism: A Single-Center Prospective Cohort Study
Authors: Zhou Yaqiong , Liu Qiting , Wang Xinquan , Wan Jindong , Liu Sen , Luo Tao , He Ping , Hou Jixin , Pu Jing , Wang Dan , Liang Dengpan , Yang Yi , Wang Peijian
Published: October 2022

Background

Superselective adrenal arterial embolization (SAAE) is an alternative treatment for patients with primary aldosteronism (PA). This single-center prospective cohort study aimed to compare the efficacy of SAAE with mineralocorticoid receptor antagonists (MRA) in treating patients with PA who refused unilateral adrenalectomy.

Methods

Of the 140 PA patients who were enrolled in the study and completed 12-month follow-up, 74 patients underwent SAAE and 66 received MRA treatment. The clinical and biochemical outcome was compared at 1, 6, and 12 months after the procedure.

Results

Baseline clinical and biochemical characteristics of the patients were similar between groups. Office, home, and ambulatory blood pressure reduction at 1 month after discharge was more pronounced in the SAAE group than MRA group (all P < 0.05) while the blood pressure reduction was comparable between the 2 groups at 6 and 12 months. Patients who underwent SAAE took less antihypertensive medications than the MRA group during 12-month follow-up (P < 0.01). Both SAAE and MRA treatment improved renin suppression, aldosterone-to-renin ratio elevation, and hypokalemia at 6 and 12 months, whereas only SAAE but not MRA reduced plasma aldosterone levels. Moreover, SAAE achieved higher rates of complete clinical and biochemical success than MRA (both P < 0.01). Logistic regression found that complete clinical and biochemical success was only directly associated with diagnosis of unilateral PA in contrast to bilateral PA (P < 0.01).

Conclusions

The present study provides evidence that SAAE is a reasonable choice of treatment in patients with either unilateral or bilateral PA in terms of clinical and biochemical outcomes. This study was registered at Chictr.org.cn (ChiCTR2100045896).
SATINN: an automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants
Authors: Yang Ran , Stendahl Alexandra M , Vigh-Conrad Katinka A , Held Madison , Lima Ana C , Conrad Donald F
Published: October 2022

Motivation

The mammalian testis is a complex organ with a cellular composition that changes smoothly and cyclically in normal adults. While testis histology is already an invaluable tool for identifying and describing developmental differences in evolution and disease, methods for standardized, digital image analysis of testis are needed to expand the utility of this approach.

Results

We developed SATINN (Software for Analysis of Testis Images with Neural Networks), a multi-level framework for automated analysis of multiplexed immunofluorescence images from mouse testis. This approach uses residual learning to train convolutional neural networks (CNNs) to classify nuclei from seminiferous tubules into seven distinct cell types with an accuracy of 81.7%. These cell classifications are then used in a second-level tubule CNN, which places seminiferous tubules into one of 12 distinct tubule stages with 57.3% direct accuracy and 94.9% within ±1 stage. We further describe numerous cell- and tubule-level statistics that can be derived from wild-type testis. Finally, we demonstrate how the classifiers and derived statistics can be used to rapidly and precisely describe pathology by applying our methods to image data from two mutant mouse lines. Our results demonstrate the feasibility and potential of using computer-assisted analysis for testis histology, an area poised to evolve rapidly on the back of emerging, spatially resolved genomic and proteomic technologies.

Availability and implementation

The source code to reproduce the results described here and a SATINN standalone application with graphic-user interface are available from http://github.com/conradlab/SATINN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Culturally Competent Policy Practice in Minority Communities during the COVID-19 Pandemic: Contextual and Structural Perspective
Authors: Nouman Hani , Tarshish Noam , Altshuler Alex
Published: October 2022

Minority communities have borne a disproportionate burden of health, social and economic consequences during the pandemic. By engaging in policy-shaping processes, social workers can contribute to the development of beneficial policies for minority communities. When working in cross-cultural environments with majorities and minorities, social workers must develop cultural competence to be effective in policy practice. Despite the importance associated with cultural competence in policy practice (CCPP), little empirical evidence exists regarding what is required of social workers in order to engage in culturally competent policy change during the pandemic. In the present study, we address this lacuna through the theoretical framework of culturally competent policy practice. Drawing on twenty-one in-depth interviews, which were conducted at two time points during the pandemic with social workers who work with ultra-Orthodox minority communities in Israel, we demonstrate that CCPP involves the combination of two perspectives—contextual and structural. These include identifying and analysing social problems from a local and global perspective, reshaping the problem through self-awareness and critical awareness of power relations, and applying cultural competence skills that reflect the unique characteristics of the communities. This article discusses the strengths and limitations of CCPP, especially when implemented in changing social and political situations.
Home dialysis in older adults: challenges and solutions
Authors: Wu Henry H L , Dhaygude Ajay P , Mitra Sandip , Tennankore Karthik K
Published: October 2022

There is a rising demand for dialysis in the older population given the increased numbers of older adults living with chronic kidney disease (CKD) progressing to kidney failure. Home dialysis, i.e. peritoneal dialysis (PD) and home hemodialysis (HHD), has been available for decades, but more recently there has been a rapid increase in home dialysis utilization as patients and clinicians consider its practical and clinical advantages. For older adults, incident home dialysis utilization more than doubled and prevalent home dialysis growth nearly doubled over the past decade. Whilst its advantages and recent rise in popularity are evident, there are numerous barriers and challenges that are important to consider prior to initiating older adults on home dialysis. Some nephrology healthcare professionals do not view home dialysis as an option for older adults. Successful delivery of home dialysis for older adults may be made even more difficult by physical or cognitive limitations, concerns around dialysis adequacy, and treatment-related complications, as well as challenges relating to caregiver burnout and patient frailty that are unique to home dialysis and older adults. Ultimately, it would be important for clinicians, patients and their caregivers to define what constitutes a ‘successful therapy’ to ensure treatment goals are aligned towards each individual's priorities of care, considering the complex challenges that surround an older adult receiving home dialysis. In this review, we evaluate some of the key challenges surrounding the delivery of home dialysis to older adults and propose potential solutions based on updated evidence to overcome these challenges.
Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps’ Genomes
Authors: Abrahim Mayla , Machado Edson , Alvarez-Valín Fernando , de Miranda Antonio Basílio , Catanho Marcos
Published: October 2022

Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.
Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies
Authors: Naranjo-Ortiz Miguel A , Molina Manu , Fuentes Diego , Mixão Verónica , Gabaldón Toni
Published: October 2022

Background

Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis, or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a nonnegligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors.

Findings

Here we present Karyon, a Python-based toolkit that uses raw sequencing data and de novo genome assembly to assess several parameters and generate informative plots to assist in the identification of nonchanonical genomic traits. Karyon includes automated de novo genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species.

Conclusions

Our results show that 10 (28.57%) of the assemblies presented signs of unusual genomic configurations, suggesting that these are common, at least for some lineages within the Fungi.
Genetic risk of osteoarthritis operates during human skeletogenesis
Authors: Rice Sarah J , Brumwell Abby , Falk Julia , Kehayova Yulia S , Casement John , Parker Eleanor , Hofer Ines M J , Shepherd Colin , Loughlin John
Published: October 2022

Osteoarthritis (OA) is a polygenic disease of older people resulting in the breakdown of cartilage within articular joints. Although it is a leading cause of disability, there are no disease-modifying therapies. Evidence is emerging to support the origins of OA in skeletogenesis. Whereas methylation quantitative trait loci (mQTLs) co-localizing with OA genome-wide association study signals have been identified in aged human cartilage and used to identify effector genes and variants, such analyses have never been conducted during human development. Here, for the first time, we have investigated the developmental origins of OA genetic risk at seven well-characterized OA risk loci, comprising 39 OA-mQTL CpGs, in human fetal limb (FL) and cartilage (FC) tissues using a range of molecular genetic techniques. We identified significant OA-mQTLs at 14 and 29 CpGs in FL and FC tissues, respectively, and compared our results with aged cartilage samples (AC). Differential methylation was observed at 26 sites between FC and AC, with the majority becoming actively hypermethylated in old age. Notably, 6/9 OA effector genes showed allelic expression imbalances during fetal development. Finally, we conducted ATAC-sequencing in cartilage from the developing and aged hip and knee to identify accessible chromatin regions and found enrichment for transcription factor binding motifs including SOX9 and FOS/JUN. For the first time, we have demonstrated the activity of OA-mQTLs and expression imbalance of OA effector genes during human skeletogenesis. We show striking differences in the spatiotemporal function of these loci, contributing to our understanding of OA aetiology, with implications for the timing and strategy of pharmacological interventions.
Covering by Planks and Avoiding Zeros of Polynomials
Authors: Glazyrin Alexey , Karasev Roman , Polyanskii Alexandr
Published: October 2022

We note that the recent polynomial proofs of the spherical and complex plank covering problems by Zhao and Ortega-Moreno give some general information on zeros of real and complex polynomials restricted to the unit sphere. As a corollary of these results, we establish several generalizations of the celebrated Bang plank covering theorem. We prove a tight polynomial analog of the Bang theorem for the Euclidean ball and an even stronger polynomial version for the complex projective space. Specifically, for the ball, we show that for every real nonzero $d$-variate polynomial $P$ of degree $n$, there exists a point in the unit $d$-dimensional ball at distance at least $1/n$ from the zero set of the polynomial $P$. Using the polynomial approach, we also prove the strengthening of the Fejes Tóth zone conjecture on covering a sphere by spherical segments, closed parts of the sphere between two parallel hyperplanes. In particular, we show that the sum of angular widths of spherical segments covering the whole sphere is at least $\pi $.
Homotopies of Constant Cuntz Class
Authors: Toms Andrew S
Published: October 2022

Let $A$ be a unital simple separable exact C$^{\ast }$-algebra that is approximately divisible and of real rank zero. We prove that the set of positive elements in $A$ with a fixed Cuntz class is path connected. This result applies in particular to irrational rotation algebras and approximately finite-dimensional (AF) algebras.
On the Existence of SRB Measures for ∞ Surface Diffeomorphisms
Authors: Buzzi Jérôme , Crovisier Sylvain , Sarig Omri
Published: October 2022

We give a proof of Viana’s [19] conjecture on physical measures, in the special case of $C^\infty $ surface diffeomorphisms, and using the analysis of entropy and Lyapunov exponents we developed in [5]. Burguet [3] has recently proved a stronger result, using a different method.
Potential for Emergence of Foodborne Trematodiases Transmitted by an Introduced Snail (Melanoides tuberculata) in California and Elsewhere in the United States
Authors: Metz Daniel C G , Turner Andrew V , Nelson Alexandria P , Hechinger Ryan F
Published: October 2022

We document that 3 human-infectious trematodes and their introduced first intermediate host snail (Melanoides tuberculata) are widespread throughout southern California. We surveyed 41 fishing localities, 19 of which harbored snails infected with zoonotic trematodes. Two of the parasites, Haplorchis pumilio and Centrocestus formosanus, are fishborne intestinal trematodes recognized as being important human pathogens in other areas of the world; the third, Philophthalmus gralli, can infect the human eye. An additional 5 species detected infecting M. tuberculata are likely of little direct threat to people; however, they may be recently introduced to the Americas, highlighting the risk that additional pathogenic trematodes transmitted by the snail in its native range could be introduced to the United States. The current, possible human-infection risk in California clarifies the need to consider the introduced snail and its parasites from a public health perspective anywhere in the United States the snail has been introduced.
In utero hyperthermia in late gestation derails dairy calf early-life mammary development
Authors: Dado-Senn Bethany M , Field Sena L , Davidson Brittney D , Dahl Geoffrey E , Laporta Jimena
Published: October 2022

Prenatal hyperthermia has immediate and long-term consequences on dairy cattle growth, immunity, and productivity. While changes in the molecular architecture are reported in the mature mammary gland (MG), any influence on early-life mammary development is unknown. Herein, we characterize the impact of late-gestation in utero heat stress on heifer mammary gross and cellular morphology at early-life developmental stages (i.e., birth and weaning). During summer, pregnant dams were exposed to environmental heat stress (shade of a free-stall barn) or offered active cooling (shade, fans, and water soakers) for 54 ± 5 d before parturition (avg. temperature–humidity index = 79). Heifer calves born to these dams were either in utero heat-stressed (IU-HT; n = 36) or in utero cooled (IU-CL; n = 37) and were managed as a single cohort thereafter. A subset of heifers was euthanized at birth (d0; n = 8/treatment; 4.6 ± 2.3 h after birth) and after weaning (d63; n = 8/treatment; 63.0 ± 1.5 d) to harvest the whole MG. An ultrasound of rear mammary parenchyma (MPAR) was taken prior to d63 and correlated to harvested MPAR cross-sectional area and weight. Portions of mammary fat pad (MFP) and MPAR were preserved for compositional and histological analysis, including ductal structure number and cross-sectional area, connective tissue area, and adipocyte number and cross-sectional area. Cellular proliferation in MPAR was assessed via Ki-67 immunohistochemistry. Relative to IU-CL heifers, the MGs of IU-HT heifers were shorter in length at d0 and d63 (P ≤ 0.02). There were moderate correlations between d63 ultrasound and harvest measures. The IU-HT heifers had reduced MG and MFP mass at d0 and d63 (P ≤ 0.05), whereas MPAR mass was reduced only at d0 (P = 0.01). IU-HT heifers had greater MPAR protein and DNA content at d63 (P ≤ 0.04), but there were no MFP compositional differences (P ≥ 0.12). At d0, IU-HT heifers had fewer MPAR ductal structures (P ≤ 0.06), but there were no differences at d63. Yet, MPAR luminal and total ductal structure cross-sectional areas of IU-HT heifers were reduced at both d0 and d63 (P ≤ 0.01). The MFP adipocytes of IU-HT heifers were smaller at d0 (P ≤ 0.01), but differences were not detected at d63. The IU-HT heifers had diminished MPAR total, stromal, and epithelial cellular proliferation at both d0 and d63 (P < 0.01). Prenatal hyperthermia derails dairy calf early-life mammary development with potential carry-over consequences on future synthetic capacity.
Nutritive value, silage fermentation characteristics, and aerobic stability of grass-legume round-baled silages at differing moisture concentrations with and without manure fertilization and microbial inoculation
Authors: Coblentz Wayne K , Akins Matthew S , Jaramillo David M , Cavadini Jason S
Published: October 2022

For baled silages, production of clostridial fermentation products can be exacerbated by exceeding normal moisture targets (45% to 55%), and/or by the application of dairy slurry before harvest. Our objectives were to test a microbial inoculant as a mitigant of clostridial products in high-moisture, grass-legume (52% ± 13.8% cool-season grasses, 44.0% ± 14.0% legumes [predominately alfalfa]) baled silages in swards that were fertilized with dairy slurry. A secondary objective was to examine the effects of bale moisture and inoculation on the aerobic stability of these fermented silages following exposure to air. After the first-cutting was removed, three manure treatments were applied as a whole-plot factor: 1) control (no manure); 2) slurry applied immediately to stubble (63,250 L/ha); or 3) slurry applied after a 1-wk delay (57,484 L/ha). An interactive arrangement of bale moisture (64.1% or 48.4%) and inoculation (yes or no) served as a subplot term in the experiment. The inoculant contained both homolactic (Lactococcus lactis 0224) and heterolactic (Lactobacillus buchneri LB1819) bacteria. The experimental design was analyzed as a randomized complete block with four replications, and the study included 48 experimental units (1.2 × 1.2-m round bales). Total fermentation acids were affected (P ≤ 0.021) by slurry application strategies, but this was likely related to inconsistent bale moisture across slurry-application treatments. Concentrations of butyric acid were low, and there were no detectable contrasts comparing manure treatments (mean = 0.05%; P ≥ 0.645). Bale moisture affected all measures of fermentation, with bales made at 64.1% moisture exhibiting a more acidic final pH (4.39 vs. 4.63; P < 0.001), less residual water-soluble carbohydrates (2.1% vs. 5.1%; P < 0.001), as well as greater lactic acid (4.64% vs. 2.46%; P < 0.001), acetic acid (2.26% vs. 1.32%; P < 0.001), and total fermentation acids (7.37% vs. 3.97%; P < 0.001). Inoculation also reduced pH (4.47 vs. 4.56; P = 0.029), and increased acetic acid (1.97% vs. 1.61%; P < 0.001) and 1,2-propanediol (1.09% vs. 0.72%; P < 0.001) compared to controls. During a 34-d aerobic exposure period, maximum surface bale temperatures were not affected (P ≥ 0.186) by any aspect of treatment, likely due to the prevailing cool ambient temperatures; however, yeast counts were numerically lower in response to greater (P < 0.001) production of acetic acid that was stimulated by both high bale moisture and inoculation.
Characterization of KDM5 lysine demethylase family substrate preference and identification of novel substrates
Authors: Hoekstra Matthew , Ridgeway Nashira H , Biggar Kyle K
Published: October 2022

The KDM5/JARID1 sub-family are 2-oxoglutarate and Fe(II)-dependent lysine-specific histone demethylases that are characterized by their Jumonji catalytic domains. The KDM5 family is known to remove tri-/di-methyl modifications from lysine-4 of histone H3 (i.e. H3-K4me2/3), a mark associated with active gene expression. As a result, studies to date have revolved around the influence of KDM5 on disease through their ability to regulate H3-K4me2/3. Recent evidence demonstrates that KDM5 may influence disease beyond H3-K4 demethylation, making it critical to further investigate KDM5-mediated demethylation of non-histone proteins. To help identify potential non-histone substrates for the KDM5 family, we developed a library of 180 permutated peptide substrates, with sequences that are systematically altered from the wild-type H3-K4me3 substrate. From this library, we characterized recombinant KDM5A/B/C/D substrate preference and developed recognition motifs for each KDM5 demethylase. The recognition motifs developed were used to predict potential substrates for KDM5A/B/C/D and profiled to generate a list of high-ranking and medium/low-ranking substrates for further in vitro validation. Through this approach, we identified 66 high-ranking substrates in which KDM5 demethylases displayed significant in vitro activity towards.
An Assessment of American Indian Forestry Research, Information Needs, and Priorities
Authors: Dockry Michael J , Hoagland Serra J , Leighton Adrian D , Durglo James R , Pradhananga Amit
Published: October 2022

Native American and Alaska Native tribes manage millions of acres of land and are leaders in forestry and fire management practices despite inadequate and inequitable funding. Native American tribes are rarely considered as research partners due to historically poor relationships with non-native scientists, tribal mistrust of research, differences between Indigenous values and scientific methods, and low Indigenous representation at research institutions. Understanding tribal research needs is critical to foster successful research partnerships with underserved tribal communities. This study expands on a 2011 tribal research needs assessment with a survey to identify tribal natural resource professionals’ research needs, access to research findings, and interest in participating in research. Information needs identified in our survey includes forest health, water quality, culturally significant species, workforce and tribal youth development, cultural importance of water, and invasive species. Additionally, postfire response and valuation, resilience and long-term forestry, protecting and curating tribal data, and Indigenous burning were more important research needs for tribal members than for nontribal members. This study can inform forestry research planning efforts and establish ­research priorities and collaborations that are aligned with needs identified by tribal natural resource managers.

Study Implications: There is a growing desire to broaden forestry research to support tribal forest management. This study shows that tribal research priorities include forest health, water quality, culturally significant species, workforce development/training, tribal youth development, cultural importance of water, and invasive species. Additionally, postfire response and valuation, resilience and long-term forestry, protecting and curating tribal data, and Indigenous burning were ranked of higher importance by tribal members than nontribal members. This study can inform federal research entities, universities, and natural resource management agencies in planning and establishing research priorities that are aligned with the needs identified by tribal resource managers.
3D photon conserving code for time-dependent general relativistic radiative transfer: CARTOON
Authors: Takahashi Mikiya M , Ohsuga Ken , Takahashi Rohta , Ogawa Takumi , Umemura Masayuki , Asahina Yuta
Published: October 2022

We develop the three-dimensional general relativistic radiative transfer code: CARTOON (Calculation code of Authentic Radiative Transfer based On phOton Number conservation in curved space–time) which is improved from the two-dimensional code: ARTIST developed by Takahashi & Umemura (2017). In CARTOON, the frequency-integrated general relativistic radiative transfer equation is solved in a photon number-conserving manner, and the isotropic and coherent scattering in the zero angular momentum observers (ZAMO) frame and the fluid rest frame is incorporated. By calculating the average energy of photons, energy conservation of the radiation is also guaranteed. With the test calculations in two-dimensional and three-dimensional space, we have demonstrated that the wavefront propagation in black hole space–time can be correctly solved in CARTOON conserving photon numbers. The position of the wavefront coincides with the analytical solution and the number of photons remains constant until the wavefront reaches the event horizon. We also solve the radiative transfer equation on the geodesic reaching the observer’s screen. The time variation of the intensity map on the observer’s screen can be simultaneously and consistently calculated with the time variation of the radiation field around the black hole. In addition, the black hole shadow can be reproduced in moderately optically thin situations.
Consequences of dynamically unstable moons in extrasolar systems
Authors: Hansen Bradley M S
Published: October 2022

Moons orbiting rocky exoplanets in compact orbits about other stars experience an accelerated tidal evolution, and can either merge with their parent planet or reach the limit of dynamical instability within a Hubble time. We review the parameter space over which moons become unbound, including the effects of atmospheric tides on the planetary spin. We find that such tides can change the final outcome from merger to escape, albeit over a limited parameter space. We also follow the further evolution of unbound moons, and demonstrate that the overwhelmingly most likely long-term outcome is that the unbound moon returns to collide with its original parent planet. The dust released by such a collision is estimated to reach optical depths $\sim 10^{-3}$, exhibit characteristic temperatures of a few hundred degrees kelvin, and last for a few thousand years. These properties make such events an attractive model for the emerging class of middle-aged main-sequence stars that are observed to show transient clouds of warm dust. Furthermore, a late collision between a planet and a returning moon on a hyperbolic orbit may sterilize an otherwise habitable planet.