bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the principles of embryonic mammary gland branching morphogenesis
Authors: Satta Jyoti P. , Lindström Riitta , Myllymäki Satu-Marja , Lan Qiang , Trela Ewelina , Prunskaite-Hyyryläinen Renata , Kaczyńska Beata , Voutilainen Maria , Kuure Satu , Vainio Seppo J. , Mikkola Marja L. 
Published: August 2024

ABSTRACT
Branching morphogenesis is a characteristic feature of many essential organs, such as the lung and kidney, and most glands, and is the net result of two tissue behaviors: branch point initiation and elongation. Each branched organ has a distinct architecture customized to its physiological function, but how patterning occurs in these ramified tubular structures is a fundamental problem of development. Here, we use quantitative 3D morphometrics, time-lapse imaging, manipulation of ex vivo cultured mouse embryonic organs and mice deficient in the planar cell polarity component Vangl2 to address this question in the developing mammary gland. Our results show that the embryonic epithelial trees are highly complex in topology owing to the flexible use of two distinct modes of branch point initiation: lateral branching and tip bifurcation. This non-stereotypy was contrasted by the remarkably constant average branch frequency, indicating a ductal growth invariant, yet stochastic, propensity to branch. The probability of branching was malleable and could be tuned by manipulating the Fgf10 and Tgfβ1 pathways. Finally, our in vivo data and ex vivo time-lapse imaging suggest the involvement of tissue rearrangements in mammary branch elongation.
N-terminal tags impair the ability of lamin A to provide structural support to the nucleus
Authors: Odell Jacob , Lammerding Jan 
Published: August 2024

ABSTRACT
Lamins are intermediate filament proteins that contribute to numerous cellular functions, including nuclear morphology and mechanical stability. The N-terminal head domain of lamin is crucial for higher order filament assembly and function, yet the effects of commonly used N-terminal tags on lamin function remain largely unexplored. Here, we systematically studied the effect of two differently sized tags on lamin A (LaA) function in a mammalian cell model engineered to allow for precise control of expression of tagged lamin proteins. Untagged, FLAG-tagged and GFP-tagged LaA completely rescued nuclear shape defects when expressed at similar levels in lamin A/C-deficient (Lmna–/–) MEFs, and all LaA constructs prevented increased nuclear envelope ruptures in these cells. N-terminal tags, however, altered the nuclear localization of LaA and impaired the ability of LaA to restore nuclear deformability and to recruit emerin to the nuclear membrane in Lmna–/– MEFs. Our finding that tags impede some LaA functions but not others might explain the partial loss of function phenotypes when tagged lamins are expressed in model organisms and should caution researchers using tagged lamins to study the nucleus.
Absence of a functional gut microbiome impairs host amino acid metabolism in the Pacific spiny dogfish (Squalus suckleyi)
Authors: MacPherson Jess , Shipley Oliver N. , Weinrauch Alyssa M. , Busquets-Vass Geraldine , Newsome Seth D. , Anderson W. Gary 
Published: August 2024

ABSTRACT
Nitrogen recycling and amino acid synthesis are two notable ways in which the gut microbiome can contribute to host metabolism, and these processes are especially important in nitrogen-limited animals. Marine elasmobranchs are nitrogen limited as they require substantial amounts of this element to support urea-based osmoregulation. However, following antibiotic-induced depletion of the gut microbiome, elasmobranchs are known to experience a significant decline in circulating urea and employ compensatory nitrogen conservation strategies such as reduced urea and ammonia excretion. We hypothesized that the elasmobranch gut microbiome transforms dietary and recycled nutrients into amino acids, supporting host carbon and nitrogen balance. Here, using stable isotope analyses, we found that depleting the gut microbiome of Pacific spiny dogfish (Squalus suckleyi) resulted in a significant reduction to the incorporation of supplemented dietary 15N into plasma amino acids, notably those linked to nitrogen handling and energy metabolism, but had no effect on gut amino acid transport. These results demonstrate the importance of gut microbes to host amino acid pools and the unique nitrogen handling strategy of marine elasmobranchs. More broadly, these results elucidate how the gut microbiome contributes to organismal homeostasis, which is likely a ubiquitous phenomenon across animal populations.
Brain energy metabolism as an underlying basis of slow and fast cognitive phenotypes in honeybees
Authors: Tait Catherine , Chicco Adam J. , Naug Dhruba 
Published: August 2024

ABSTRACT
In the context of slow–fast behavioral variation, fast individuals are hypothesized to be those who prioritize speed over accuracy while slow individuals are those which do the opposite. Since energy metabolism is a critical component of neural and cognitive functioning, this predicts such differences in cognitive style to be reflected at the level of the brain. We tested this idea in honeybees by first classifying individuals into slow and fast cognitive phenotypes based on a learning assay and then measuring their brain respiration with high-resolution respirometry. Our results broadly show that inter-individual differences in cognition are reflected in differences in brain mass and accompanying energy use at the level of the brain and the whole animal. Larger brains had lower mass-specific energy usage and bees with larger brains had a higher metabolic rate. These differences in brain respiration and brain mass were, in turn, associated with cognitive differences, such that bees with larger brains were fast cognitive phenotypes whereas those with smaller brains were slow cognitive phenotypes. We discuss these results in the context of the role of energy in brain functioning and slow–fast decision making and speed accuracy trade-off.
Un breve diálogo entre decolonización y estudios organizacionales en Venezuela
Authors: González Durán Egberto Jose , El Zailah Bernal Dauwy Yoselin 
Published: August 2024

Este trabajo busca contribuir al debate entre la decolonización y los estudios organizacionales (OE) en Venezuela, abriendo las puertas a las múltiples formas de hacer las cosas y no desde la mejor. Se aborda desde la impronta colonizadora, para cuyo análisis se utiliza una metodología reflexiva desde una revisión bibliográfica. Versa sobre dos temas: el boom petrolero, la colonización y sus resultados, y los eo en Venezuela y la necesidad de la decolonización desde la mirada organizacional. De esta forma, el tema petrolero como fenómeno organizacional en un país con rezagos desde el siglo XIX y con cultura rural permitirá comprender la cultura dominada por lo “moderno”, traído desde Estados Unidos y Reino Unido. La bonanza económica resultante de la explotación petrolera en un país monoproductor mostrará la marginalización del conocimiento. Son variados los fenómenos organizacionales que surgieron del fenómeno organizacional petrolero, por lo que la decolonización epistemológica, desde las bases de los EO como anarquías organizadas dentro del significado polisémico de la organización, será una herramienta indispensable para deconstruir y reconstruir la organización emergente del siglo XXI.
Facilitating Compromise in Redistricting with Transfer Distance Midpoints
Authors: Dobbs Kiera W. , King Douglas M. , Ludden Ian G. , Jacobson Sheldon H. 
Published: August 2024

States in the United States redraw their electoral district boundaries every 10 years. This redistricting process can be contentious and has long-lasting consequences for political representation. To reduce bias in the redistricting process, some states require bipartisan commissions; however, bipartisan commissions can still involve partisan tension if the political parties cannot compromise. We propose an optimization framework to facilitate compromise between two redistricting stakeholders. This framework seeks a midpoint between two stakeholder plans with respect to a distance metric. A midpoint can help the stakeholders visualize a potential compromise that incorporates district structure common to both of their proposed plans. First, we consider multiple distance metrics and evaluate whether midpoints with respect to these metrics are achievable and align with redistricting requirements. Then we formulate a mixed-integer linear program to find a midpoint (or any fractional point) between two given plans with respect to the transfer distance. This formulation incorporates district structure from both given plans by fixing variables; consequently, it is possible to solve some realistically sized instances exactly in reasonable amounts of time. We present experiments on grid instances and Missouri’s congressional redistricting instance to demonstrate how this method can quickly generate compromise options that align with redistricting requirements. Funding: This material is based on work supported by the National Science Foundation Graduate Research Fellowship Program [Grant DGE-1746047]. Supplemental Material: The online appendix is available at https://doi.org/10.1287/ijoo.2023.0029 .
Multimodal mucosal and systemic immune characterization of a non-human primate trachoma model highlights the critical role of local immunity during acute phase disease
Authors: Paulet Elodie , Contreras Vanessa , Galhaut Mathilde , Rosenkrands Ida , Holland Martin , Burton Matthew , Dietrich Jes , Gallouet Anne-Sophie , Bosquet Nathalie , Relouzat Francis , Langlois Sébastien , Follmann Frank , Le Grand Roger , Labetoulle Marc , Rousseau Antoine 
Published: August 2024

Background
Trachoma is a leading cause of infection-related blindness worldwide. This disease is caused by recurrent Chlamydia trachomatis (Ct) infections of the conjunctiva and develops in two phases: i) active (acute trachoma, characterized by follicular conjunctivitis), then long-term: ii) scarring (chronic trachoma, characterized by conjunctival fibrosis, corneal opacification and eyelid malposition). Scarring trachoma is driven by the number and severity of reinfections. The immune system plays a pivotal role in trachoma including exacerbation of the disease. Hence the immune system may also be key to developing a trachoma vaccine. Therefore, we characterized clinical and local immune response kinetics in a non-human primate model of acute conjunctival Ct infection and disease.

Methodology/Principal findings
The conjunctiva of non-human primate (NHP, Cynomolgus monkeys—Macaca fascicularis-) were inoculated with Ct (B/Tunis-864 strain, B serovar). Clinical ocular monitoring was performed using a standardized photographic grading system, and local immune responses were assessed using multi-parameter flow cytometry of conjunctival cells, tear fluid cytokines, immunoglobulins, and Ct quantification. Clinical findings were similar to those observed during acute trachoma in humans, with the development of typical follicular conjunctivitis from the 4th week post-exposure to the 11th week. Immunologic analysis indicated an early phase influx of T cells in the conjunctiva and elevated interleukins 4, 8, and 5, followed by a late phase monocytic influx accompanied with a decrease in other immune cells, and tear fluid cytokines returning to initial levels.

Conclusion/Significance
Our NHP model accurately reproduces the clinical signs of acute trachoma, allowing for an accurate assessment of the local immune responses in infected eyes. A progressive immune response occurred for weeks after exposure to Ct, which subsided into a persistent innate immune response. An understanding of these local responses is the first step towards using the model to assess new vaccine and therapeutic strategies for disease prevention.
Low Prevalence of Reporting of Participant Race and Ethnicity in Gastroenterology Research Publications
Authors: Burton-Murray Helen , Vélez Christopher , Boyd Taylor , Garcia-Fischer Isabelle , Paz Mary , Weeks Imani , Kiser Katheryn , Chan Andrew T. 
Published: August 2024

INTRODUCTION:
Empirical information on the evolution of reporting race and ethnicity information in gastroenterology research is lacking. To facilitate understanding of where improvements are needed to increase diversity, equity, and inclusion in gastroenterology research, we aimed to evaluate reporting and representation by race and ethnicity in studies published in flagship US-based gastroenterology journals over 20 years.

METHODS:
We manually reviewed reporting and representation by race and ethnicity in all original research articles published in the American Journal of Gastroenterology and Gastroenterology in 2000, 2010, and 2020.

RESULTS:
Of 1,168 publications, 24% reported information on race/ethnicity, significantly more commonly reported in US-based study samples vs non-US-based samples. While reporting significantly increased over time, reporting rates were still low as of 2020 (37% overall; 54% with US-based samples).

DISCUSSION:
We recommend that gastroenterology journals create standard reporting requirements for sociodemographic information, including information on race, ethnicity, and/or cultural background.
Bisphosphonates for the prevention of osteoporotic fractures in postmenopausal women with osteopenia: a systematic review and meta-analysis
Authors: Yureneva S. V. , Averkova V. G. 
Published: August 2024

BACKGROUND: The lack of sufficient systematization of data on the use of bisphosphonates for primary prevention of osteoporotic fractures in postmenopausal women with osteopenia prompted us to conduct a systematic review with meta-analysis of publications devoted to this problem.AIM: To study the effect of bisphosphonates on bone mineral density (BMD), markers of bone metabolism and fractures in postmenopausal women with osteopenia. MATERIALS AND METHODS: A total of 1140 potentially eligible articles were found in the initial publication screening. From the initially identified results, 13 studies were meta-analyzed. The design of the studies selected for meta-analysis was consistent with randomized controlled trials. RESULTS: On average, study bisphosphonate preparations compared with placebo increased lumbar spine BMD by 5.54 % (95 % CI 4.44–6.63, I2 = 93.65 %), total hip BMD by 4.53 % (95 % CI 3. 2–5.86, I2=96.32 %), femoral neck BMD by 3.63 % (95 % CI 1.5–5.75, I2=95.9 %), total body BMD by 3.25 % (95 % CI 2.28–4.22, I2=87.87 %), proximal femur BMD by 4.76 % (95 % CI 3.43–6.08, I2 = 88.64 %). There was a statistically significant effect of bisphosphonates on low-energy fractures (OR 0.62; 95 % CI 0.49–0.77), clinical vertebral fractures (OR 0.51; 95 % CI 0.38–0.69), and radiologically confirmed vertebral fractures (OR 0.63; 95 % CI 0.4–0.98). CONCLUSION: These results obtained allow us to conclude that bisphosphonates (alendronate, zolendronic acid, ibandronate, resedronate) have a positive therapeutic effect, and their administration is justified in postmenopausal women with osteopenia for the prevention of osteoporotic fractures and increase in BMD.
On 𝐿𝑝 boundedness of rough Fourier integral operators
Authors: Wu Guoning , Yang Jie 
Published: August 2024

Abstract
In this paper, we deal with the

L
p

L^{p}

boundedness of rough Fourier integral operators

T

a
,
φ

T_{a,\varphi}

with amplitude

a
⁢

(
x
,
ξ
)

∈

L
∞

⁢

S
ρ
m

a(x,\xi)\in L^{\infty}S_{\rho}^{m}

and phase function

φ
⁢

(
x
,
ξ
)

∈

L
∞

⁢

Φ
2

\varphi(x,\xi)\in{L^{\infty}}{\Phi^{2}}

which satisfies a measure condition.
We show that

T

a
,
φ

T_{a,\varphi}

is bounded on

L
p

L^{p}

for

1
≤
p
≤
∞

1\leq p\leq\infty

if

m
<

n
⁢

(

ρ
−
1

)

p

−

ρ
⁢

(

n
−
1

)

2
⁢
p

m<\frac{n(\rho-1)}{p}-\frac{\rho(n-1)}{2p}

when

1
≤
p
≤
2

1\leq p\leq 2

or

m
<

n
⁢

(

ρ
−
1

)

2

−

ρ
⁢

(

n
−
1

)

2

⁢

(

1
−

1
p

)

m<\frac{n(\rho-1)}{2}-\frac{\rho(n-1)}{2}(1-\frac{1}{p})

when

2
≤
p
≤
∞

2\leq p\leq\infty

.
Our main results extend and improve some known results about

L
p

L^{p}

boundedness of Fourier integral operators.
α-, β- and γ-duals of the sequence spaces formed by a regular matrix of Tetranacci numbers
Authors: Khan Izhar Ali , Meitei Mayanglambam Udoy 
Published: August 2024

AbstractThe primary objective of this paper is to create a novel infinite Toeplitz matrix by leveraging Tetranacci numbers. This matrix serves as the foundation for defining new sequence spaces denoted asc0⁢(G){c_{0}(G)},c⁢(G){c(G)},ℓ∞⁢(G){\ell_{\infty}(G)}, andℓp⁢(G){\ell_{p}(G)}, where1≤p<∞{1\leq p<\infty}. By utilizing this newly constructed matrix, the paper also explores and examines various algebraic and topological properties inherent to the sequence spacesc0⁢(G){c_{0}(G)},c⁢(G){c(G)},ℓ∞⁢(G){\ell_{\infty}(G)}, andℓp⁢(G){\ell_{p}(G)}for values ofpwithin the range of1≤p<∞{1\leq p<\infty}. At last, we also prove existence theorem with example for infinite systems of differential equations inℓp⁢(G){\ell_{p}(G)}.
Increase in the frequency of melanism in Abert’s Squirrel in Boulder, Colorado
Authors: Barrett Lake H. , Nunes Christian A. , Lehtinen Richard M. 
Published: August 2024

Abstract
In the northern portions of its range, Abert’s Squirrel (Sciurus aberti) has two color morphs: a wild-type gray morph and a melanistic morph. Using camera traps, citizen science data and in-person observations in and near Boulder, Colorado (USA), we compared current color morph frequencies to those reported in a 1969–1971 study. At all study sites, we observed a large and statistically significant increase in the frequency of the melanistic morph compared to historic data. We hypothesize that this increase may be due to selection favoring the melanistic morph in a changing forest environment.
Hermite-Hadamard-type inequalities for generalized trigonometrically and hyperbolic ρ-convex functions in two dimension
Authors: Dragomir Silvestru Sever , Jleli Mohamed , Samet Bessem 
Published: August 2024

Abstract
In this article, we establish Hermite-Hadamard-type inequalities for the two classes of functions

X

±
λ

(

Ω

)

=

{

f
∈

C

2

(

Ω

)

:
Δ
f
±
λ
f
≥
0

}

{X}_{\pm \lambda }\left(\Omega )=\{f\in {C}^{2}\left(\Omega ):\Delta f\pm \lambda f\ge 0\}

, where

λ
>
0

\lambda \gt 0

and

Ω

\Omega

is an open subset of

R

2

{{\mathbb{R}}}^{2}

. We also obtain a characterization of the set

X

−
λ

(

Ω

)

{X}_{-\lambda }\left(\Omega )

. Notice that in the one-dimensional case, if

Ω
=
I

\Omega =I

(an open interval of

R

{\mathbb{R}}

) and

λ
=

ρ

2

\lambda ={\rho }^{2}

,

ρ
>
0

\rho \gt 0

, then

X

λ

(

Ω

)

{X}_{\lambda }\left(\Omega )

(resp.

X

−
λ

(

Ω

)

{X}_{-\lambda }\left(\Omega )

) reduces to the class of functions

f
∈

C

2

(

I

)

f\in {C}^{2}\left(I)

such that

f

f

is trigonometrically

ρ

\rho

-convex (resp. hyperbolic

ρ

\rho

-convex) on

I

I

.
Random walk algorithms for solving nonlinear chemotaxis problems
Authors: Sabelfeld Karl K. , Bukhasheev Oleg 
Published: August 2024

Abstract
Random walk based stochastic simulation methods for solving a nonlinear system of coupled transient diffusion and drift-diffusion equations governing a two-component chemotaxis process are developed.
The nonlinear system is solved by linearization, the system is evolved in time, by small time steps, where on each step a linear system of equations is solved by using the solution from the previous time step.
Three different stochastic algorithms are suggested, (1) the global random walk on grid (GRWG), (2) a randomized vector algorithm (RVA) based on a special transformation of the original matrix to a stochastic matrix, and (3) a stochastic projection algorithm (SPA). To get high precision results, these methods are combined with an iterative refinement method.
The slice sampler and centrally symmetric distributions
Authors: Planas Christophe , Rossi Alessandro 
Published: August 2024

Abstract
We show that the slice sampler generates Markov chains whose variables are mean independent and thus uncorrelated when the target density is centrally symmetric. Skewness instead boosts correlations. Popular implementation algorithms such as stepping-out and multivariate-sampling-with-hyperrectangles add statistical inefficiency, the first in case of multimodality, the second in all circumstances. A new sampler which exploits these structural and algorithmic characteristics to reduce the variance of Monte Carlo estimates is experimented in several sampling problems. An insight into the properties of the product slice sampler is also provided.
Integrating deep convolutional surrogate solvers and particle swarm optimization for efficient inverse design of plasmonic patch nanoantennas
Authors: Hemayat Saeed , Moayed Baharlou Sina , Sergienko Alexander , Ndao Abdoulaye 
Published: August 2024

Abstract
Plasmonic nanoantennas with suitable far-field characteristics are of huge interest for utilization in optical wireless links, inter-/intrachip communications, LiDARs, and photonic integrated circuits due to their exceptional modal confinement. Despite its success in shaping robust antenna design theories in radio frequency and millimeter-wave regimes, conventional transmission line theory finds its validity diminished in the optical frequencies, leading to a noticeable void in a generalized theory for antenna design in the optical domain. By utilizing neural networks, and through a one-time training of the network, one can transform the plasmonic nanoantennas design into an automated, data-driven task. In this work, we have developed a multi-head deep convolutional neural network serving as an efficient inverse-design framework for plasmonic patch nanoantennas. Our framework is designed with the main goal of determining the optimal geometries of nanoantennas to achieve the desired (inquired by the designer) S
11 and radiation pattern simultaneously. The proposed approach preserves the one-to-many mappings, enabling us to generate diverse designs. In addition, apart from the primary fabrication limitations that were considered while generating the dataset, further design and fabrication constraints can also be applied after the training process. In addition to possessing an exceptionally rapid surrogate solver capable of predicting S
11 and radiation patterns throughout the entire design frequency spectrum, we are introducing what we believe to be the pioneering inverse design network. This network enables the creation of efficient plasmonic antennas while concurrently accommodating customizable queries for both S
11 and radiation patterns, achieving remarkable accuracy within a single network framework. Our framework is capable of designing a wide range of devices, including single band, dual band, and broadband antennas, with directivities and radiation efficiencies reaching 11.07 dBi and 75 %, respectively, for a single patch. The proposed approach has been developed as a transformative shift in the inverse design of photonics components, with its impact extending beyond antenna design, opening a new paradigm toward real-time design of application-specific nanophotonic devices.