bluuebunny/crossref_metadata_2025 huggingface dataset:
Simple measurement of the pressure dependence of density for fatty acid esters
Authors: Yamawaki Hiroshi
Published: May 2023

A simple variable-volume method using a polytetrafluoroethylene capsule as a sample cell was applied to measure the pressure dependence of liquid density (ρ). The method was applied to 2-ethylhexyl benzoate at 313, 333, and 353 K, and the reproducibility of its volume change was confirmed at pressures of up to 400 MPa. A correction term for the apparatus was also estimated. The uncertainty in the high-pressure ρ measurements was estimated to be ∼±1%. Using the developed method, the ρ values of methyl laurate at pressures of up to 400 MPa at 313 and 333 K, as well as those of methyl linoleate at pressures of up to 400 MPa at 313, 333, and 353 K, were measured. The results were in good agreement with the literature values in the low-pressure range. The proposed method enables the determination of the high-pressure ρ of liquids with greater ease than previously possible.
In situ catalytic cells for x-ray absorption spectroscopy measurement
Authors: Mei Bingbao , Sun Fanfei , Wei Yao , Zhang Hao , Chen Xing , Huang Weifeng , Ma Jingyuan , Song Fei , Jiang Zheng
Published: May 2023

In catalysis, determining the relationship between the dynamic electronic and atomic structure of the catalysts and the catalytic performance under actual reaction conditions is essential to gain a deeper understanding of the reaction mechanism since the structure evolution induced by the absorption of reactants and intermediates affects the reaction activity. Hard x-ray spectroscopy methods are considered powerful and indispensable tools for the accurate identification of local structural changes, for which the development of suitable in situ reaction cells is required. However, the rational design and development of spectroscopic cells is challenging because a balance between real rigorous reaction conditions and a good signal-to-noise ratio must be reached. Here, we summarize the in situ cells currently used in the monitoring of thermocatalysis, photocatalysis, and electrocatalysis processes, focusing especially on the cells utilized in the BL14W1-x-ray absorption fine structure beamline at the Shanghai Synchrotron Radiation Facility, and highlight recent endeavors on the acquisition of improved spectra under real reaction conditions. This review provides a full overview of the design of in situ cells, aiming to guide the further development of portable and promising cells. Finally, perspectives and crucial factors regarding in situ cells under industrial operating conditions are proposed.
Explosive crystallization of amorphous germanium-tin films by irradiation with a 3-keV electron beam
Authors: Nakamura R. , Miyamoto M. , Ishimaru M.
Published: May 2023

Much effort has been expended to obtain thin films of metastable solid solutions of germanium (Ge) that contain as high tin (Sn) content as possible because of their excellent electronic and optoelectronic properties. On the basis of our previous study on amorphous Ge, we demonstrated in this study that irradiation of substrate-free films of amorphous Ge100−xSnx (x = 8, 11, and 19 at. %) with a low-energy electron beam of 3 keV at ambient temperature can induce instantaneous wide-area crystallization (explosive crystallization). Characteristic spiral crystal growth associated with explosive crystallization occurred with areas exceeding 50 μm in diameter around a scanned area of the electron beam of 8 × 8 μm2. As a result, solid solutions of GeSn with Sn concentration up to 19 at. % were obtained with the suppression of precipitation of β-Sn. The region of explosive crystallization reduced in size with increasing Sn content. In addition, thermal analyses revealed that the heat released during crystallization of amorphous GeSn films decreased with increasing Sn content. This relationship indicates that the heat release at the growth front plays a key role in the propagation of explosive crystallization of a-GeSn.
Momentum work and the energetic foundations of physics. II. The ideal gas law derived via processes
Authors: Kalies Grit , Do Duong D. , Arnrich Steffen
Published: May 2023

In Paper I of this series, the elastic collision was described via simultaneous processes, where the energy is conserved at any moment. In this paper, we critically review the kinetic theory of gases, which was developed based on Newtonian mechanics, and show that it violates the principle of the conservation of energy. By placing the energy conservation at the beginning of the deductive formalism, we derive the ideal gas law via equally strong simultaneous counter-processes at the walls, namely, momentum work and volume work. Several new insights into the state variables of an ideal gas are obtained: (i) pressure cannot be expressed via the kinetic energy of an ideal gas, and (ii) temperature can be interpreted as a particle-related (microscopic) state variable. The historical choice to set a zero point of the potential energy for a confined ideal gas needs to be corrected, and the internal energy of an ideal gas turns out to include more forms of energy than specified in the kinetic theory of gases. Finally, and importantly, we show that the process approach to an ideal gas and thus to collisions is experimentally confirmed.
Contactium: A strongly correlated model system
Authors: Cioslowski Jerzy , Englert Berthold-Georg , Trappe Martin-Isbjörn , Hue Jun Hao
Published: May 2023

At the limit of an infinite confinement strength ω, the ground state of a system that comprises two fermions or bosons in harmonic confinement interacting through the Fermi–Huang pseudopotential remains strongly correlated. A detailed analysis of the one-particle description of this “contactium” reveals several peculiarities that are not encountered in conventional model systems (such as the two-electron harmonium atom, ballium, and spherium) involving Coulombic interparticle interactions. First of all, none of the natural orbitals (NOs) {ψn(ω;r)} of the contactium is unoccupied, which implies nonzero collective occupancies for all the angular momenta. Second, the NOs and their non-ascendingly ordered occupation numbers {νn} turn out to be related to the eigenfunctions and eigenvalues of a zero-energy Schrödinger equation with an attractive Gaussian potential. This observation enables the derivation of their properties, such as the n−4/3 asymptotic decay of νn at the n→∞ limit (which differs from that of n−8/3 in the Coulombic systems), the independence of the confinement energy vn=⟨ψn(ω;r)|12ω2r2|ψn(ω;r)⟩ of n, and the n−2/3 asymptotic decay of the respective contribution νntn to the kinetic energy. Upon suitable scaling, the weakly occupied NOs of the contactium turn out to be virtually identical to those of the two-electron harmonium atom at the ω → ∞ limit, despite the entirely different interparticle interactions in these systems.
Flow-induced vibration of a cylinder-plate assembly in laminar flow: Branching behavior
Authors: Lien Fue-Sang , Yee Eugene
Published: May 2023

The transverse flow-induced vibration of an elastically supported cylinder-plate assembly (viz., a rigid splitter-plate attached to the downstream side of a circular cylinder) with a low mass ratio of 10 and a zero structural damping coefficient at a Reynolds number of 100 is investigated in the present work. A careful identification of all the branches in the amplitude response of an assembly with various plate lengths is undertaken, in conjunction with the associated flow dynamics responsible for these branches involving various aspects of the flow, such as the vortex-shedding in the far wake and the evolution of the shear layers generated on the upper and lower surfaces of the cylinder in the near wake. This knowledge offers crucial new perspectives on the nature and physical mechanisms behind the complex dynamics of a cylinder-plate system. These investigations involve a wide range of plate lengths LSP/D=0–4 (where D is the diameter of the circular cylinder) over an extensive span of reduced velocities Ur = 2–30. For LSP/D≤0.5, a self-limiting oscillation is induced in the structure—this can be either a vortex-induced vibration (VIV) or an integrated VIV-galloping response. For LSP/D≥0.75, the amplitude response is non-limited in the sense that the amplitude increases linearly with increasing Ur. More precisely, the amplitude response consists of either a strongly correlated VIV-galloping regime (at LSP/D=0.75) or two clearly separated regimes of VIV and galloping (for LSP/D>0.75). In the galloping regime, both odd- and even-multiple synchronizations between the system oscillation and the vortex shedding are supported. “Kinks” in the amplitude response signal the onset of synchronization branches in the galloping regime. Two new branches have been identified for a cylinder-plate assembly with longer plate lengths, namely, an initial galloping branch and a still (quiescent) branch. The initial galloping branch is associated with wake meandering. For the still branch, the assembly is stationary (no vibratory motion), and flow over the assembly is steady (no vortex shedding or shear-layer meandering).
Computational study of rarefied gas flow and heat transfer in lid-driven cylindrical cavities
Authors: Roohi Ehsan , Ebrahimi Amin
Published: May 2023

The gas flow characteristics in lid-driven cavities are influenced by several factors, such as the cavity geometry, gas properties, and boundary conditions. In this study, the physics of heat and gas flow in cylindrical lid-driven cavities with various cross sections, including fully or partially rounded edges, is investigated through numerical simulations using the direct simulation Monte Carlo (DSMC) and the discrete unified gas kinetic scheme (DUGKS) methods. The thermal and fluid flow fields are systematically studied for both constant and oscillatory lid velocities, for various degrees of gas rarefaction ranging from the slip to the free-molecular regimes. The impact of expansion cooling and viscous dissipation on the thermal and flow fields, as well as the occurrence of counter-gradient heat transfer (also known as anti-Fourier heat transfer) under non-equilibrium conditions, is explained based on the results obtained from numerical simulations. Furthermore, the influence of the incomplete tangential accommodation coefficient on the thermal and fluid flow fields is discussed. A comparison is made between the thermal and fluid flow fields predicted in cylindrical cavities and those in square-shaped cavities. The present work contributes to the advancement of micro-/nano-electromechanical systems by providing valuable insight into rarefied gas flow and heat transfer in lid-driven cavities.
Squirming with a backward-propelling cage
Authors: Della-Giustina J. , Nganguia H. , Demir E.
Published: May 2023

A squirmer enclosed in a droplet represents a minimal model for some drug delivery systems. In the case of a spherical squirmer swimming with a spherical cage in a Newtonian fluid [Reigh et al., “Swimming with a cage: Low-Reynolds-number locomotion inside a droplet,” Soft Matter 13, 3161 (2017)], it was found that the squirmer and droplet always propelled in the same direction albeit at different speeds. We expand the model to include particles' shape and medium's heterogeneity, two biologically relevant features. Our results reveal a novel behavior: a configuration that consists of a spherical squirmer and a spheroidal droplet in highly heterogeneous media yields a backward motion of the droplet.
Gβγ
activates
PIP2
hydrolysis by recruiting and orienting
PLCβ
on the membrane surface
Authors: Falzone Maria E. , MacKinnon Roderick
Published: May 2023

Phospholipase C-βs (PLCβs)
catalyze the hydrolysis of phosphatidylinositol 4, 5–bisphosphate

(
P
I
P
2
)

into

inositoltriphosphate

(
IP3
)

and

diacylglycerol

 

(
DAG
)

.

P
I
P
2

regulates the activity of many membrane proteins, while
IP3
and
DAG
lead to increased intracellular Ca
2+
levels and activate protein kinase C, respectively.
PLCβs
are regulated by G protein–coupled receptors through direct interaction with

G
α

q

and

G
β
γ

and are aqueous-soluble enzymes that must bind to the cell membrane to act on their lipid substrate. This study addresses the mechanism by which

G
β
γ

activates
PLCβ
3. We show that
PLCβ
3 functions as a slow Michaelis–Menten enzyme ( 

k

cat

∼
2
 

s

-
1

,
 
K

M

∼
0.43
 
m
o
l
%

 ) on membrane surfaces. We used membrane partitioning experiments to study the solution-membrane localization equilibrium of
PLCβ
3. Its partition coefficient is such that only a small quantity of 
PLCβ
3 exists in the membrane in the absence of

G
β
γ

 . When

G
β
γ

is present, equilibrium binding on the membrane surface increases
PLCβ
3 in the membrane, increasing

V

max

in proportion. Atomic structures on membrane vesicle surfaces show that two

G
β
γ

anchor 
PLCβ
3 with its catalytic site oriented toward the membrane surface. Taken together, the enzyme kinetic, membrane partitioning, and structural data show that

G
β
γ

activates

PLCβ

by increasing its concentration on the membrane surface and orienting its catalytic core to engage

P
I
P
2

 . This principle of activation explains rapid stimulated catalysis with low background activity, which is essential to the biological processes mediated by

P
I
P
2

, IP3
, and
DAG
.
The variable use of first-person-singular subject forms during an
academic year abroad
Authors: Gudmestad Aarnes , Edmonds Amanda
Published: May 2023

The goal of the current study was to investigate
the variable use and development of first-person-singular subject
forms in additional-language Spanish before and at the end of an
academic year in Spain. Our data came from the LANGSNAP corpus (http://langsnap.soton.ac.uk). We examined oral
semi-guided interviews from 16 participants. We coded all contexts
of first-person-singular subject forms, either the personal pronoun
yo or an unexpressed subject
(K = 3,571), for 11 independent variables. Our
mixed-effects model showed that a range of linguistic factors
(polarity, clause type, referent continuity, and perseveration) and
individual characteristics (engagement with English and placement
type) impacted the variable use of first-person-singular subjects
and that the use of these subject forms changed over the course of
an academic year in Spain.
From the spatial ego to cognitive control
Authors: Leon Guerrero Sibylla , Luk Gigi
Published: May 2023

Ellen Bialystok’s early work from 1976–1988 has
had a lasting influence on the fields of bilingualism and
linguistics. This chapter reviews her seminal work establishing
bilingualism as a cross-disciplinary area of study in 1976. It then
explores Bialystok’s language processing research of the 1980’s,
articulating two of her crucial, yet often overlooked achievements.
First, Bialystok’s early information processing models for
word-level representations set the stage for an explosion of
cognitive bilingualism research by identifying cognitive processes
involved in second language acquisition. Second, her work set a
precedent for understanding the spectrum of language experiences and
their complexities, providing essential insight into why even subtle
distinctions should be considered and reported when describing
bilinguals. Presciently, Bialystok’s early work anticipated current
understandings and future directions for bilingualism research,
making her sustained contributions to the area an invaluable asset
for continued exploration.
Bilingual cognitive differences within the context of
socioeconomic status
Authors: Brito Natalie H.
Published: May 2023

This chapter investigates bilingualism and
cognitive skills, specifically memory, for infants and young
children. For the young developmental samples, memory is not a
unitary construct, but one that requires attention and cognitive
flexibility as they navigate through the complex environments around
them. Bilingualism, being a language and social experience, also
interacts with broader contexts, such as socioeconomic status (SES)
in some communities. In this chapter, I examine how exposure to
language(s) and SES is associated with broader memory generalization
during infancy. The unique and interacting contribution of
bilingualism and SES on cognition reveals the need to consider
multiple experiences in order to gain a realistic and more
comprehensive understanding of cognitive development.
Metalinguistic awareness in bilinguals
Authors: Friesen Deanna C. , Lamoureux Chastine
Published: May 2023

The goal of this chapter is to outline Ellen
Bialystok’s contribution to our understanding of metalinguistic
awareness development. We start by describing both her work in the
field and her cognitive framework that outlines the components
(i.e., linguistic analysis & control) needed to successfully
perform metalinguistic tasks. We then describe the impact of this
theoretical approach on subsequent research on metalinguistic
awareness in bilinguals and monolinguals. Finally, we outline how
direct instruction in metalinguistic awareness can be informed by
considering the importance of developing both linguistic analysis
and control in the classroom.
Bilingualism and functional connectivity
Authors: Anderson John A.E.
Published: May 2023

Four patterns describe how bilingualism affects
the functional connectivity of the brain. First, a general
observation across most of the studies I surveyed was that
bilinguals tended to have higher functional connectivity when
compared to monolinguals. Second, increased connectivity with the
salience network, a set of regions including the anterior cingulate
cortex, the bilateral insula, and subcortical regions is often
associated with language training or language
diversity where proactive attention to content is paramount. Third,
to the degree that individuals have greater exposure or mastery of a
second language, (greater proficiency and an earlier or simultaneous
age of acquisition) and can rely more on reactive control, studies
often show greater bilateral connectivity between the inferior
frontal gyri. This is also sometimes associated with decreased
activation of frontal regions implying distributed load and greater
neural efficiency. The distributed neural pattern in young adulthood
may also explain how bilingual older adults are able to sustain
their cognition at levels of neuropathology most monolinguals cannot
endure. Fourth, in studies that examined anticorrelations between
task and rest networks, bilinguals tended to have more distinct
(e.g., modular organization), and more strongly anticorrelated
task-positive and default-mode networks, and this was often
correlated with cognitive control.
Bilingualism and brain structure
Authors: Pliatsikas Christos
Published: May 2023

The study of the effects of bilingualism on
brain structure has gained significant traction in the last decade,
naturally following the pioneering work by Ellen Bialystok and
others on the effects of bilingualism on cognition. However, despite
the general interest and enthusiasm about the related evidence, the
field of bilingualism-induced structural brain plasticity remains
young and relatively unexplored. At the same time, this field has
been largely limited to young and healthy populations. This chapter
revisits and reviews the evidence about bilingualism-induced
neuroplasticity and the contemporary theories that provide
explanations of the available evidence, with a particular focus on
the ageing and patient bilingual brain. Specifically, a full account
of the reported effects on healthy ageing bilinguals is provided,
followed by the limited findings from diseases that cause
progressive brain decline, such as mild cognitive impairment,
Alzheimer’s and Huntington’s diseases, epilepsy, and multiple
sclerosis. The chapter concludes with some suggestions for future
directions for the field.
Determination of cooperatively rearranging regions in a binary glass former
Authors: Mizuguchi T , Odagaki T
Published: May 2023

Cooperative motions are important for understanding the divergence of viscosity of glassy materials at a finite temperature, since the elementary process of the structural relaxation occurs within the smallest cooperative region as suggested by Adam and Gibbs. On the basis of the definition of a cooperatively rearranging region (CRR) by Adam and Gibbs and by Odagaki, we determine the size of CRR for the Kob–Andersen model as a function of temperature using molecular dynamics simulations. We first confine particles in a spherical region and, varying the radius of that region, we determine the CRR size as the smallest radius of the region in which particles can change their relative positions. The size of the CRR increases as the temperature is reduced and seems to diverge below the glass transition temperature. The temperature dependence of the number of particles in the CRR obeys the equation derived from the Adam–Gibbs relation and the Vogel–Fulcher–Tammann equation.
Interaction potential of two nonidentical ground-state atoms
Authors: Peng Yan , Cheng Shijing , Zhou Wenting
Published: May 2023

We study the interaction potential of two nonidentical ground-state atoms coupled to a scalar field in a vacuum by separately calculating the contributions of vacuum fluctuations and those of the radiation reaction of the atoms. Both cases of atoms in a free space and in parallel or vertical alignment to a reflecting boundary are considered. For the former case, we find that the leading-order interaction potential in the region λ

A
≪ L ≪ λ

B
exhibits the same separation-dependence as that in the region L ≪ λ

A
≪ λ

B
, where L, λ

A
and λ

B
are respectively the interatomic separation and the transition wavelengths of two atoms with λ

A
≪ λ

B
. For the latter case, we find that boundary-induced modifications are very remarkable when L ≫ z, with z characterizing the separation between the two-atom system and the boundary. Particularly, when L further satisfies L ≫ λ

A
and L ≫ λ

B
, the interaction potential in the parallel- and the vertical-alignment cases respectively scales as z
4
L
−7 and z
2
L
−5, the L-dependence of which is one order higher than those of two atoms in regions where L ≫ z and meanwhile L ≪ λ

A
or/and L ≪ λ

B
. Our results suggest that retardation for the interaction potential of two nonidentical atoms with remarkably distinctive transition frequencies happens only when the interatomic separation is much greater than the transition wavelengths of both atoms.
Atomistic simulations of graphene origami: Dynamics and kinetics
Authors: Zhang Panpan , Jia Haihong , Zhang Yan-Fang , Du Shixuan
Published: May 2023

Origami offers two-dimensional (2D) materials with great potential for applications in flexible electronics, sensors, and smart devices. However, the dynamic process, which is crucial to construct origami, is too fast to be characterized by using state-of-the-art experimental techniques. Here, to understand the dynamics and kinetics at the atomic level, we explore the edge effects, structural and energy evolution during the origami process of an elliptical graphene nano-island (GNI) on a highly ordered pyrolytic graphite (HOPG) substrate by employing steered molecular dynamics simulations. The results reveal that a sharper armchair edge is much easier to be lifted up and realize origami than a blunt zigzag edge. The potential energy of the GNI increases at the lifting-up stage, reaches the maximum at the beginning of the bending stage, decreases with the formation of van der Waals overlap, and finally reaches an energy minimum at a half-folded configuration. The unfolding barriers of elliptical GNIs with different lengths of major axis show that the major axis should be larger than 242 Å to achieve a stable single-folded structure at room temperature. These findings pave the way for pursuing other 2D material origami and preparing origami-based nanodevices.
Type II multiferroic order in two-dimensional transition metal halides from first principles spin-spiral calculations
Authors: Sødequist Joachim , Olsen Thomas
Published: May 2023

We present a computational search for spin spiral ground states in two-dimensional transition metal halides that are experimentally known as van der Waals bonded bulk materials. Such spin spirals break the rotational symmetry of the lattice and lead to polar ground states where the axis of polarization is strongly coupled to the magnetic order (type II multiferroics). We apply the generalized Bloch theorem in conjunction with non-collinear density functional theory calculations to find the spiralling vector that minimizes the energy and then include spin–orbit coupling to calculate the preferred orientation of the spin plane with respect to the spiral vector. We find a wide variety of magnetic orders ranging from ferromagnetic, stripy anti-ferromagnetic, 120∘ non-collinear structures and incommensurate spin spirals. The latter two introduce polar axes and are found in the majority of materials considered here. The spontaneous polarization is calculated for the incommensurate spin spirals by performing full supercell relaxation including spinorbit coupling and the induced polarization is shown to be strongly dependent on the orientation of the spiral planes. We also test the effect of Hubbard corrections on the results and find that for most materials LDA + U results agree qualitatively with LDA. An exception is the Mn halides, which are found to exhibit incommensurate spin spiral ground states if Hubbard corrections are included whereas bare LDA yields a 120∘ non-collinear ground state.
Integrated modelling techniques to implication of demographic change and urban expansion dynamics on water demand management of developing city in Lake Hawassa Watershed, Ethiopia
Authors: Kassay Abreham Birhane , Tuhar Abraham Woldemichael , Ulsido Mihret Dananto
Published: May 2023

Hawassa is a rapidly developing city in the Lake Hawassa watershed of Ethiopia that is a continuous change in the face of an urban environment. The urban development has been increasing the challenge to maintain urban services and surrounding environmental quality. These exert a new challenge to the growing gap between urban water demand and supply balance. Correlating urban growth and water demand to a rapidly growing population remains imperative to adaptive urban planning and decision-making. This study quantified urban development with demographic change and urban expansion dynamics. The population statistics and satellite imageries of historical years 1991–2021 and projections to the year 2051 were analysed using the exponential increase model and geospatial techniques. Multiple empirical modelling approaches were employed to link urban water demand with the explanatory variable. The study findings revealed the projected urban population reach more than one million and 79.2% of urbanization by 2051. With the current trend of 8.9% built-up growth rate, urban area will cover 73.6 km2 (45.9%) for the predicted period. The demographic variables and the sprawl of urban expansion jointly influence the water demand with statistically significant (f = 0.000, at α = 0.05) association. An increase in urban water use efficiency also reduces the water demand by increasing the availability of water supplies. Thus, the proposed model can be applied to reset the emerging relationship between the explanatory variables and water demand management. A detailed consideration of the spatially explicit effect on access to and optimization of the urban water supply system is vital to a local-specific solution. Integrating urban land planning with water demand management, therefore, has the potential to minimize the need to construct additional water supply infrastructure and cheer a sustainable urban environment.
Effect of flax fiber orientation in carbon-flax fiber composite on tensile and visco elastic behavior
Authors: Uppin Vinayak S , Gouda P S Shivakumar , Sridhar I , Vastrad Jyoti V
Published: May 2023

This paper deals with the effect of Flax fiber orientations on the tensile and viscoelastic response of Carbon/Flax hybrid composite. The composite laminates were prepared by varying flax fiber orientations of [0°4F/0°1C]1, [+30°2F/0°1C/−30°2F]1,[+45°2F/0°1C/−45°2F]1,[+60°2F/0°1C/−60°2F]1,and [+75°2F/0°1C/−75°2F]1using the Hot press compression molding technique. The tensile and DMA (Dynamic Mechanical Analyzer) tests have been done for evaluating strength, strain to failure, toughness and storage and loss modulus, and also the damping factor of the laminates. The maximum tensile strength of 262 MPa was observed for 0-Degree oriented Flax fiber Carbon epoxy laminates. However, a decrease in tensile strength was noticed as the Flax fiber orientation increased from 0-Degree to 75-Degree. The maximum strain of 7.5% was induced in the 30-Degree Flax fiber carbon composite. Additionally, it was noticed that the rotation of fibers during load applied is the main cause for inducing additional strain to failure of Flax fibers. Changes in the storage modulus, loss modulus, and, damping factor were also observed for different flax fiber orientations.
Solving 𝑆-unit, Mordell, Thue, Thue–Mahler and Generalized Ramanujan–Nagell Equations via the Shimura–Taniyama Conjecture
Authors: von Känel Rafael , Matschke Benjamin
Published: May 2023

In the first part we construct algorithms (over

Q

\mathbb {Q}

) which we apply to solve

S
S

-unit, Mordell, cubic Thue, cubic Thue–Mahler and generalized Ramanujan–Nagell equations. As a byproduct we obtain alternative practical approaches for various classical Diophantine problems, including the fundamental problem of finding all elliptic curves over

Q

\mathbb {Q}

with good reduction outside a given finite set of rational primes. The first type of our algorithms uses modular symbols, and the second type combines explicit height bounds with efficient sieves. In particular we construct a refined sieve for

S
S

-unit equations which combines Diophantine approximation techniques of de Weger with new geometric ideas. To illustrate the utility of our algorithms we determined the solutions of large classes of equations, containing many examples of interest which are out of reach for the known methods. In addition we used the resulting data to motivate various conjectures and questions, including Baker’s explicit

a
b
c

abc

-conjecture and a new conjecture on

S
S

-integral points of any hyperbolic genus one curve over

Q

\mathbb {Q}

.

In the second part we establish new results for certain old Diophantine problems (e.g. the difference of squares and cubes) related to Mordell equations, and we prove explicit height bounds for cubic Thue, cubic Thue–Mahler and generalized Ramanujan–Nagell equations. As a byproduct, we obtain here an alternative proof of classical theorems of Baker, Coates and Vinogradov–Sprindžuk. In fact we get refined versions of their theorems, which improve the actual best results in many fundamental cases. We also conduct some effort to work out optimized height bounds for

S
S

-unit and Mordell equations which are used in our algorithms of the first part. Our results and algorithms all ultimately rely on the method of Faltings (Arakelov, Paršin, Szpiro) combined with the Shimura–Taniyama conjecture, and they all do not use lower bounds for linear forms in (elliptic) logarithms.

In the third part we solve the problem of constructing an efficient sieve for the

S
S

-integral points of bounded height on any elliptic curve

E
E

over

Q

\mathbb {Q}

with given Mordell–Weil basis of

E
(

Q

)

E(\mathbb {Q})

. Here we combine a geometric interpretation of the known elliptic logarithm reduction (initiated by Zagier) with several conceptually new ideas. The resulting “elliptic logarithm sieve” is crucial for some of our algorithms of the first part. Moreover, it considerably extends the class of elliptic Diophantine equations which can be solved in practice: To demonstrate this we solved many notoriously difficult equations by combining our sieve with known height bounds based on the theory of logarithmic forms.
A note on numerical radius attaining mappings
Authors: Jung Mingu
Published: May 2023

We prove that if every bounded linear operator (or

N
N

-homogeneous polynomials) on a Banach space

X
X

with the compact approximation property attains its numerical radius, then

X
X

is a finite dimensional space. Moreover, we present an improvement of the polynomial James’ theorem for numerical radius proved by Acosta, Becerra Guerrero and Galán [Q. J. Math. 54 (2003), pp. 1–10]. Finally, the denseness of weakly (uniformly) continuous

2
2

-homogeneous polynomials on a Banach space whose Aron-Berner extensions attain their numerical radii is obtained.
Renal Medullary Overexpression of Sphingosine-1-Phosphate Receptor 1 Transgene Attenuates Deoxycorticosterone Acetate (DOCA)-Salt Hypertension
Authors: Hu Gaizun , Xie Dengpiao , Chen Chaoling , Wang Weili , Li Pin-Lan , Ritter Joseph K , Li Ningjun
Published: May 2023

BACKGROUND

Our previous studies showed that renal medullary sphingosine-1-phosphate receptor 1 (S1PR1) mediated sodium excretion, high salt intake increased S1PR1 level, deoxycorticosterone acetate (DOCA) blocked high salt-induced S1PR1 in the renal medulla, and that conditional knockout of S1PR1 in the collecting duct aggravated DOCA-salt hypertension. The present study tested the hypothesis that overexpression of S1PR1 transgene in the renal medulla attenuates the sodium retention and hypertension in DOCA-salt mouse model.

METHODS

Male C57BL/6J mice received renal medullary transfection of control or S1PR1-expressing plasmids and then DOCA-salt treatment. Renal sodium excretion and arterial pressure were compared between control and S1PR1-overexpressed mice in response to high salt loading or pressure natriuresis.

RESULTS

S1PR1-transfected mice showed significantly enhanced urinary sodium excretion in response to acute sodium loading (0.93 ± 0.27 in control vs. 4.72 ± 1.12 µmol/min/gKW in S1PR1-overexpressed mice, P < 0.05) and the pressure natriuresis (3.58 ± 1.77 vs. 9.52 ± 1.38, P < 0.05), less positive sodium balance in response to chronic high-salt intake (3.05 ± 0.39 vs. 1.65 ± 0.39 mmol/72 hr, P < 0.05), and consequently, the attenuation of DOCA-salt hypertension (134.2 ± 6.79 vs. 109.8 ± 3.54 mm Hg, P < 0.05). The αENaC protein amount in the renal medulla was not changed, however, the βENaC was significantly decreased and the γENaC was significantly increased in S1PR1-overexpressed mice. The immunostaining showed apical membrane translocation of γENaC, while no change of αENaC and βENaC in control mice, and that the apical membrane translocation of γENaC was blocked in S1PR1-treasffected mice.

CONCLUSIONS

These results suggested that activation of S1PR1 in the renal medulla attenuates DOCA-induced sodium retention and salt-sensitive hypertension associated with inhibition of ENaC.
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning
Authors: Luo Ling , Wei Chih-Hsuan , Lai Po-Ting , Leaman Robert , Chen Qingyu , Lu Zhiyong
Published: May 2023

Motivation

Biomedical named entity recognition (BioNER) seeks to automatically recognize biomedical entities in natural language text, serving as a necessary foundation for downstream text mining tasks and applications such as information extraction and question answering. Manually labeling training data for the BioNER task is costly, however, due to the significant domain expertise required for accurate annotation. The resulting data scarcity causes current BioNER approaches to be prone to overfitting, to suffer from limited generalizability, and to address a single entity type at a time (e.g. gene or disease).

Results

We therefore propose a novel all-in-one (AIO) scheme that uses external data from existing annotated resources to enhance the accuracy and stability of BioNER models. We further present AIONER, a general-purpose BioNER tool based on cutting-edge deep learning and our AIO schema. We evaluate AIONER on 14 BioNER benchmark tasks and show that AIONER is effective, robust, and compares favorably to other state-of-the-art approaches such as multi-task learning. We further demonstrate the practical utility of AIONER in three independent tasks to recognize entity types not previously seen in training data, as well as the advantages of AIONER over existing methods for processing biomedical text at a large scale (e.g. the entire PubMed data).

Availability and implementation

The source code, trained models and data for AIONER are freely available at https://github.com/ncbi/AIONER.
ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data
Authors: Moshiri Niema
Published: May 2023

Motivation

In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. However, as the number of samples that are sequenced grows rapidly, compute resources needed to reconstruct consensus genomes can become prohibitively large.

Results

ViralConsensus is a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data. ViralConsensus is orders of magnitude faster and more memory-efficient than existing methods. Further, unlike existing methods, ViralConsensus can pipe data directly from a read mapper via standard input and performs viral consensus calling on-the-fly, making it an ideal tool for viral sequencing pipelines.

Availability and implementation

ViralConsensus is freely available at https://github.com/niemasd/ViralConsensus as an open-source software project.
Efficacy and safety of dupilumab in patients with severe chronic hand eczema with inadequate response or intolerance to alitretinoin: a randomized, double-blind, placebo-controlled phase IIb proof-of-concept study
Authors: Voorberg Angelique N , Kamphuis Esmé , Christoffers Wietske A , Schuttelaar Marie L A
Published: May 2023

Background

Effective treatment options for patients with chronic hand eczema (CHE) are scarce. Dupilumab is licensed for the treatment of moderate-to-severe atopic dermatitis and has shown promising results for the treatment of hand eczema in other studies.

Objectives

To evaluate the efficacy and safety of dupilumab in adult patients with severe CHE (subtypes recurrent vesicular hand eczema or chronic fissured hand eczema) who have an inadequate response/intolerance to alitretinoin, or when alitretinoin is medically inadvisable.

Methods

In this 16-week, randomized, double-blind, placebo-controlled proof-of-concept phase IIb trial, patients with severe CHE were randomized 2 : 1 to dupilumab 300 mg or placebo subcutaneously every 2 weeks. Patients visited the outpatient clinic at the initiation of the study drug, and every 4 weeks until 16 weeks of treatment. The primary endpoint was the proportion of patients achieving at least a 75% improvement on the Hand Eczema Severity Index score (HECSI-75) at week 16. Adverse events were monitored during each visit. The study was registered on ClinicalTrials.gov (identifier NCT04512339).

Results

In total, 30 patients were randomized, and 29 patients received the assigned study drug (dupilumab n = 20, placebo n = 9). At week 16, more patients achieved HECSI-75 in the dupilumab group than in the placebo group {95% [95% confidence interval (CI) 73.1–99.7] vs. 33% [95% CI 9.0–69.1]}. Dupilumab also showed greater least square mean percentage change from baseline to week 16 in peak pruritus Numerical Rating Scale compared with placebo [−66.5 ± 10.7 (95% CI −88.6 to −44.5) vs. −25.3 ± 17.0 (95% CI −60.1–9.4)]. Adverse events were similar for the dupilumab and placebo groups and were mostly mild. There were no serious adverse events, nor did any of the adverse events lead to discontinuation of the study drug.

Conclusions

Dupilumab was efficacious and well tolerated. Larger studies of longer duration are needed to provide more evidence on the ­efficacy of dupilumab in CHE. Moreover, larger studies could also enable comparisons between clinical subtypes or aetiological ­diagnoses.
Whole-body cryotherapy as a treatment for chronic medical conditions?
Authors: Tabisz Hanna , Modlinska Aleksandra , Kujawski Sławomir , Słomko Joanna , Zalewski Pawel
Published: May 2023

Introduction

Whole-body cryotherapy (WBC) is a controlled exposure of the whole body to cold to gain health benefits. In recent years, data on potential applications of WBC in multiple clinical settings have emerged.

Sources of data

PubMed, EBSCO and Clinical Key search using keywords including terms ‘whole body’, ‘cryotherapy’ and ‘cryostimulation’.

Areas of agreement

WBC could be applied as adjuvant therapy in multiple conditions involving chronic inflammation because of its potent anti-inflammatory effects. Those might include systemic inflammation as in rheumatoid arthritis. In addition, WBC could serve as adjuvant therapy for chronic inflammation in some patients with obesity.

Areas of controversy

WBC probably might be applied as an adjuvant treatment in patients with chronic brain disorders including mild cognitive impairment and general anxiety disorder and in patients with depressive episodes and neuroinflammation reduction as in multiple sclerosis. WBC effects in metabolic disorder treatment are yet to be determined. WBC presumably exerts pleiotropic effects and therefore might serve as adjuvant therapy in multi-systemic disorders, including myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).

Growing points

The quality of studies on the effects of WBC in the clinical setting is in general low; hence, randomized controlled trials with adequate sample size and longer follow-up periods are needed.

Areas are timely for developing research

Further studies should examine the mechanism underlying the clinical efficacy of WBC. Multiple conditions might involve chronic inflammation, which in turn could be a potential target of WBC. Further research on the application of WBC in neurodegenerative disorders, neuropsychiatric disorders and ME/CFS should be conducted.
Gene expression changes reveal the impact of the space environment on the skin of International Space Station astronauts
Authors: Gu Xuefeng , Han Yuru , Shao Yue , Ma Wenhao , Shao Zeguo , Wan Guoqing , Lu Changlian , Shi Shuo , Lu Wenli
Published: May 2023

Background

The various types of ionizing radiation and altered gravity in the space environment present a risk to humans during space missions. Changes in the space environment lead to skin diseases, affecting the status of the aviators to fly. Therefore, it is important to explore the molecular-level changes in the skin during space missions.

Objectives

Bioinformatics analysis of gene arrays from hair follicle tissue of 10 astronauts was performed to explore changes in gene expression before, during and after space missions.

Methods

First, STEM (Short Time-series Expression Miner) software was used to identify the expression patterns of hair follicle genes of astronauts pre-, in- and postflight. Gene Ontology Enrichment Analysis was then performed to explore the gene functions within the module. Protein–protein interaction network analysis was performed on skin-related genes. The transcriptional regulatory network within the module was constructed using the TRRUST database. The circadian rhythm-related genes within the module were screened using the MSigDB (Molecular Signatures Database).

Results

Based on differential expression analysis between the two groups, there were 327 differentially expressed genes after the astronauts entered space compared with preflight, and only 54 differentially expressed genes after returning to Earth. This outcome suggests that the expression of most genes can be recovered on return to the ground, but there are a small number of genes whose expression cannot be recovered in a short period of time. Based on time series analysis, 311 genes showed increased expression on entry into space and decreased expression on return to Earth. The genes of this expression pattern were associated with skin development, keratinocyte differentiation and cornification. Ten hub genes were identified as skin-related genes within the module, as well as nine transcription factors and three circadian genes. One hundred and seventy-nine genes decreased in expression after entry into space and increased on return to Earth. By reviewing the literature, we found that four of the genes, CSCD2, HP, CXCR1 and SSTR4, are associated with skin diseases.

Conclusions

Through bioinformatics analysis, we found that the space environment affects skin keratinocyte differentiation, leading to skin barrier damage and inflammatory responses, and that this effect was decreased after return to Earth.
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes
Authors: Swint-Kruse Liskin , Dougherty Larissa L , Page Braelyn , Wu Tiffany , O’Neil Pierce T , Prasannan Charulata B , Timmons Cody , Tang Qingling , Parente Daniel J , Sreenivasan Shwetha , Holyoak Todd , Fenton Aron W
Published: May 2023

Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family—pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization—including quantitative evaluation of allosteric regulation—of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms.

Database URL https://github.com/djparente/PYK-DB
Complex cross-incompatibility in morning glories is consistent with a role for mating system in plant speciation
Authors: Rifkin Joanna L , Ostevik Kate L , Rausher Mark D
Published: May 2023

Reproductive isolation between selfing and outcrossing species can arise through diverse mechanisms, some of which are directly associated with differences in mating system. We dissected cross-incompatibility between the highly selfing morning glory Ipomoea lacunosa and its mixed-mating sister species Ipomoea cordatotriloba. We found that cross-incompatibility is complex, with contributions acting both before and after fertilization. We then investigated whether the transition in mating system may have facilitated the evolution of these reproductive barrier components through mismatched floral morphology, differences in reproductive context, or both. We found evidence that morphological mismatch likely contributes to reproductive isolation in at least one cross-direction and that other pollen–pistil interactions are present. We also identified hybrid seed inviability consistent with the predictions of the weak-inbreeder, strong-outbreeder hypotheses, suggesting endosperm misregulation plays an important role in cross-incompatibility. In contrast, we did not find evidence consistent with the prezygotic weak-inbreeder, strong-outbreeder hypothesis. Our study highlights the complexity of reproductive isolation between outcrossing and selfing species and the extent to which evolutionary consequences of mating system transitions can facilitate speciation.