bluuebunny/crossref_metadata_2025 huggingface dataset:
Surviving the storm: exploring the role of natural transformation in nutrition and DNA repair of stressed
Deinococcus radiodurans
Authors: Sharma Dhirendra Kumar , Soni Ishu , Rajpurohit Yogendra Singh
Published: December 2024

Deinococcus radiodurans
, a natural transformation (NT)-enabled bacterium renowned for its exceptional radiation resistance, employs unique DNA repair and oxidative stress mitigation mechanisms as a strategic response to DNA damage. This study excavates into the intricate roles of NT machinery in the stressed
D. radiodurans
, focusing on the genes
comEA
,
comEC
,
endA
,
pilT
, and
dprA
, which are instrumental in the uptake and processing of extracellular DNA (eDNA). Our data reveal that NT not only supports the nutritional needs of
D. radiodurans
under stress but also has roles in DNA repair. The study findings establish that NT-specific proteins (ComEA, ComEC, and endonuclease A [EndA]) may contribute to support the nutritional requirements in unstressed and heavily DNA-damaged cells, while DprA contributes differently and in a context-dependent manner to navigating through the DNA damage storm. Thus, this dual functionality of NT-specific genes is proposed to be a contributing factor in the remarkable ability of
D. radiodurans
to survive and thrive in environments characterized by high levels of DNA-damaging agents.

IMPORTANCE

Deinococcus radiodurans
is a bacterium known for its extraordinary radiation resistance. This study explores the roles of NT machinery in the radiation-resistant bacterium
Deinococcus radiodurans
, focusing on the genes
comEA
,
comEC
,
endA
,
pilT
, and
dprA
. These genes are crucial for the uptake and processing of eDNA and contribute to the bacterium nutritional needs and DNA repair under stress. The findings suggest that the NT-specific proteins ComEA, ComEC, and EndA may help meet the nutritional needs of unstressed and heavily DNA-damaged cells, whereas DprA plays a distinct role that varies, depending on the context in aiding cells to cope with DNA damage. The functionality of NT genes is proposed to enhance
D. radiodurans
survival in environments with high levels of DNA-damaging agents.
Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments
Authors: Howland Katie E. , Mouradian Jack J. , Uzarski Donald R. , Henson Michael W. , Uzarski Donald G. , Learman Deric R.
Published: December 2024

Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.

IMPORTANCE

The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.
Two rice cultivars recruit different rhizospheric bacteria to promote aboveground regrowth after mechanical defoliation
Authors: Jiang Changjin , Wang Fei , Tian Jinling , Zhang Wanyuan , Xie Kabin
Published: December 2024

Plants have evolved the ability to regrow after mechanical defoliation and environmental stresses. However, it is unclear whether and how defoliated plants exploit beneficial microbiota from the soil to promote aboveground regrowth. Here, we compared the defoliation-triggered changes in the root exudation and bacterial microbiome of two rice cultivars (
Oryza sativa
L
ssp
.),
indica/xian
cultivar Minghui63 and
japonica/geng
cultivar Nipponbare. The results show that reciprocal growth promotion existed between defoliated Minghui63 seedlings and soil bacteria. After the leaves were removed, the Minghui63 seedlings displayed approximately 1.5- and 2.1-fold higher root exudation and leaf regrowth rates, respectively, than did the Nipponbare seedlings. In field trials, Minghui63 and Nipponbare enriched taxonomically and functionally distinct bacteria in the rhizosphere and root. In particular, Minghui63 rhizosphere and root communities depleted bacteria whose functions are related to xenobiotics biodegradation and metabolism. The microbiome data implied that the bacterial family
Rhodocyclaceae
was specifically enriched during the regrowth of defoliated Minghui63 rice. We further isolated a
Rhodocyclaceae
strain,
Uliginosibacterium gangwonense
MDD1, from rice root. Compared with germ-free conditions, MDD1 inoculation promoted the aboveground regrowth of defoliated Minghui63 by 61% but had a weaker effect on Nipponbare plants, suggesting cultivar-specific associations between regrowth-promoting bacteria and rice. This study provides novel insight into microbiota‒root‒shoot communication, which is implicated in the belowground microbiome and aboveground regrowth in defoliated rice. These data will be helpful for microbiome engineering to increase rice resilience to defoliation and environmental stresses.

IMPORTANCE

As sessile organisms, plants face a multitude of abiotic and biotic stresses which often result in defoliation. To survive, plants have evolved the ability to regrow leaves after stresses and wounding. Previous studies revealed that the rhizosphere microbiome affected plant growth and stress resilience; however, how belowground microbiota modulates the aboveground shoot regrowth is unclear. To address this question, we used rice, an important crop worldwide, to analyze the role of rhizosphere microbiota in leaf regrowth after defoliation. Our data indicate mutual growth promotion between defoliated rice and rhizosphere bacteria and such beneficial effect is cultivar specific. The microbiome analysis also led us to find a
Uliginosibacterium gangwonense
strain that promoted rice cv. MH63 leaf regrowth. Our findings therefore present a novel insight into plant-microbiome function and provide beneficial strains that potentially enhance rice stress resilience.
Health policy to address disease-related malnutrition: a scoping review
Authors: Ford Katherine L , Basualdo-Hammond Carlota , Nasser Roseann , Avdagovska Melita , Keller Heather , Malone Ainsley , Bauer Judy D , Correia M Isabel T D , Cardenas Diana , Gramlich Leah
Published: December 2024

Background

Health policies promote optimal care, yet policies that address disease-related malnutrition (DRM) are lacking. The purpose of this study was to conduct a scoping review to identify literature on existing and planned policy to address DRM in children or adults and explore the settings, contexts and actors of DRM policy.

Methods

A search strategy comprising DRM and policy keywords was applied to eight databases on 24 February 2023. Articles that addressed DRM and policy were selected for inclusion after two independent reviews. The health policy triangle (HPT) framework (ie, actors, content, contexts and processes considerations for policy) guided data extraction and thematic analysis.

Results

A total of 67 articles were included out of the 37 196 identified. Some articles (n=14) explored established policies at the local level related to food and mealtime, nutrition care practices, oral nutritional supplement prescribing or reimbursement. Other articles gave direction or rationale for DRM policy. As part of the HPT, actors included researchers, advocacy groups and DRM champions while content pertained to standard processes for nutrition care such as screening, assessment, intervention and monitoring. Contexts included acute care and care home settings with a focus on paediatrics, adults, older adults. Processes identified were varied and influenced by the type of policy (eg, local, national, international) and its goal (eg, advocating, developing, implementing).

Discussion

There is a paucity of global DRM policy. Nutrition screening, assessment, intervention and monitoring are consistently identified as important to DRM policy. Decision makers are important actors and should consider context, content and processes to develop and mobilise DRM policy to improve nutrition care. Future efforts need to prioritise the development and implementation of policies addressing DRM.
Lymphoid enhancer-binding factor 1 (LEF1) immunostaining as a surrogate for β-catenin (CTNNB1) mutations
Authors: Hewer Ekkehard , Fischer Pascal David , Vassella Erik , Knabben Laura , Imboden Sara , Mueller Michael D , Rau Tilman T , Dettmer Matthias S
Published: December 2024

Aims

Mutations affecting exon 3 of the β-catenin (CTNNB1) gene result in constitutive activation of WNT signalling and are a diagnostic hallmark of several tumour entities including desmoid-type fibromatosis. They also define clinically relevant tumour subtypes within certain entities, such as endometrioid carcinoma. In diagnostics, β-catenin immunohistochemistry is widely used as a surrogate forCTNNB1mutations. Yet, it is often difficult to assess in practice, given that the characteristic nuclear translocation may be focal or hard to distinguish from the spillover of the normal membranous staining.

Methods

We therefore examined lymphoid enhancer-binding factor 1 (LEF1) immunostaining, a nuclear marker of WNT activation that serves as a potential surrogate forCTNNB1mutations.

Results

In a cohort of endometrial carcinomas with known mutation status (n=130) LEF1 was 85% accurate in predictingCTNNB1mutation status (64% sensitivity, 90% specificity) while β-catenin was 76% accurate (72% sensitivity; 77% specificity). Across a variety of entities characterised byCTNNB1mutations as putative drivers, we found diffuse and strong expression of LEF1 in 77% of cases. LEF1 immunostaining proved easier to interpret than β-catenin immunostaining in 54% of cases, more difficult in 1% of cases and comparable in the remaining cases.

Conclusion

We conclude that LEF1 immunostaining is a useful surrogate marker forCTNNB1mutations. It favourably complements β-catenin immunohistochemistry and outperforms the latter as a single marker.
Aortic and arterial manifestations and clinical features inTGFB3-related heritable thoracic aortic disease: results from the Montalcino Aortic Consortium
Authors: Lim Michelle Su-Anne , Guo Dong-Chuan , Velasco Torrez Walter , Lai Andrew , Schweber Jonathan , Garg Nikita , Fleischer Julie , Boileau Catherine , De Backer Julie , Evangelista Artur , Jondeau Guillaume , Le Goff Carine , Milleron Olivier , Muiño-Mosquera Laura , Morris Shaine , Ouzounian Maral , Cervi Elena , Marcadier Julien , Caffarelli Anthony , Shalhub Sherene , Pyeritz Reed , Yetman Angela , Milewicz Dianna , Braverman Alan C
Published: December 2024

Background

Pathogenic variants inTGFB3may lead to a syndromic genetic aortopathy. Heritable thoracic aortic disease (HTAD) and arterial events may occur inTGFB3-related disease but there are limited outcomes data on vascular events in this condition.

Methods

Clinical data, phenotypical features and aortic outcomes in individuals with pathogenic/likely pathogenic (P/LP)TGFB3variants enrolled in the Montalcino Aortic Consortium registry were reviewed.

Results

34 individuals (56% male, median age 42 years, IQR 17–49, range 3–74 years) with P/LPTGFB3variants were studied. Craniofacial, cutaneous and musculoskeletal features seen in Loeys-Dietz syndrome were variably present. Extra-aortic cardiovascular features included arterial tortuosity (25%), extra-aortic arterial aneurysms (6%) and mitral valve prolapse (21%).

Aortic dilation (Z-Score>2) was present in 10 individuals (29%) and aortic dissection occurred in 2 (6%). Type A aortic dissection occurred in two patients (aged between 55 years and 60 years), and one of these patients experienced a type B aortic dissection 6 years later. Seven adults (median age 62 years, range 32–69 years) with aortic root dilation (41–49 mm) are being followed. No patients have undergone prophylactic aortic surgery. Twenty-five per cent of children have aortic dilation. Sixty-eight per cent of the entire cohort remains free of aortic disease. No deaths have occurred.

Conclusions

TGFB3-related HTAD is characterised by late-onset and less penetrant thoracic aortic and arterial disease compared with other transforming growth factor β HTAD. Based on our data, a larger aortic size threshold for prophylactic aortic surgery is appropriate in patients withTGFB3-related HTAD compared with HTAD due toTGFBR1orTGFBR2variants.
Climate-sensitive models of tree mortality based on lifetime analysis and irregular permanent-plot remeasurements
Authors: Fortin Mathieu , Riofrío José , de Melo Lara Climaco , Ashiq Muhammad Waseem , Sharma Mahadev , Howard Christina , Eskelson Bianca N.I.
Published: December 2024

Climate change has driven forest growth modellers to develop different climate sensitivity implementations (CSIs) for their models. Among others, a model can rely on annual climate variables or average climate variables, such as 30-year normals. The novelty of this study was to develop a framework based on lifetime analysis to enable annual or average CSI in empirical models of tree mortality. Using this framework, we compared models of individual tree mortality based on an annual CSI with similar models relying on two average CSIs, one using interval-averaged climate variables, and the other, 30-year normals. We fitted these models to permanent-plot data of eight species in Ontario and tested the effects of summer and winter temperature as well as spring and summer precipitation in the models. Our results showed that the annual CSI was not superior to the average CSIs, but could be a valid alternative for some species. Warmer winter temperature was detrimental to the survival of Betula papyrifera, Picea glauca, and Pinus strobus, whereas greater spring and summer precipitation resulted in greater mortality occurrence for Picea mariana, Pinus banksiana, and Populus tremuloides. In most cases, the effects of climate variables were contrary to our initial hypotheses. We conclude that the effects of climate on tree mortality occurrence interact with other factors such as species distribution and ecophysiology.
Exploring SMEFT couplings using the forward–backward asymmetry in neutral current Drell–Yan production at the LHC
Authors:   the xFitter Developers’ team, Abdolmaleki Hamed , Amoroso Simone , Britzger Daniel , Dattola Filippo , Fiaschi Juri , Giuli Francesco , Glazov Alexander , Hautmann Francesco , Luszczak Agnieszka , Monfared Sara Taheri , Olness Fred , Vazzoler Federico , Zenaiev Oleksandr , Anataichuk Andrii , Moch Sven-Olaf
Published: December 2024

Neutral current Drell–Yan (DY) lepton-pair production is considered to study Z-boson quark couplings. Using the open-source fit platform , we investigate the impact of high-statistics measurements of the neutral current DY (NCDY) forward–backward asymmetry

$$A_{\textrm{FB}}$$

A
FB

near the weak boson mass scale in the present and forthcoming stages of the Large Hadron Collider (LHC). Besides recovering earlier results on the

$$A_{\textrm{FB}}$$

A
FB

sensitivity to parton distribution functions, we analyze the precision determination of Z-boson couplings to left-handed and right-handed u-quarks and d-quarks, and explore Beyond-Standard-Model contributions using the Standard Model Effective Field Theory (SMEFT) framework. We perform a sensitivity study and comment on the role of the

$$A_{\textrm{FB}}$$

A
FB

asymmetry for the electroweak SMEFT fit and precision Z-boson physics at the LHC and high-luminosity HL-LHC.
Stationary BTZ space-time in Ricci-inverse and $$f({\mathcal {R}})$$ gravity theories
Authors: Ahmed Faizuddin , Bouzenada Abdelmalek
Published: December 2024

In this paper, we explore a stationary BTZ space-time within the framework of modified gravity theory, specifically focusing on Ricci-inverse gravity. It is important to clarify that “Ricci-inverse” refers to the inverse of the Ricci tensor, not the Ricci scalar. We consider a general class of this gravity theory, where the function f is defined by

$$f({\mathcal {R}}, {\mathcal {A}}, A^{\mu \nu }\,A_{\mu \nu })$$

f
(
R
,
A
,

A

μ
ν

A

μ
ν

)

, with

$${\mathcal {R}}$$

R

and

$${\mathcal {A}}$$

A

representing the Ricci and anti-curvature scalars, respectively and

$$A^{\mu \nu }$$

A

μ
ν

is the anti-curvature tensor. We demonstrate that stationary BTZ space-time is a valid solution in this gravity theory, wherein the cosmological constant undergoes modifications due to the coupling constants. Moreover, we study another modified gravity theory known as

$$f({\mathcal {R}})$$

f
(
R
)

-gravity and analyze the stationary BTZ space-time. Subsequently, we fully integrate the geodesic equations for BTZ space-time constructed within the Ricci-Inverse gravity, expressing the solutions in terms of elementary functions and compared with the GR result. We classify different types of geodesics, including null and time-like geodesics, under three conditions: (i) nonzero mass and angular momentum,

$$M \ne 0, J\ne 0$$

M
≠
0
,
J
≠
0

, (ii) massless BTZ space-time,

$$M=0$$

M
=
0

and

$$J=0$$

J
=
0

, and (iii)

$$M=-1, J=0$$

M
=
-
1
,
J
=
0

, that is

$$AdS_3$$

A
d

S
3

-type, and analyze the results in modified gravity theories and compare with the general relativity case.
Fermion dark matter in the vector scotogenic model: a survey of signatures
Authors: Areyuna C Paulo , Zamora-Saa Jilberto , Zerwekh Alfonso R.
Published: December 2024

In this work, we have studied the vector scotogenic model in the context of the dark matter problem. Due to unitarity considerations, we have focused on the scenario with fermion dark matter, finding out that co-annihilations play a fundamental role in achieving dark matter relic abundance. Moreover, the coannihilation effects allow to separate the parameter space into two regions with different phenomenology. In addition, we have studied the detection prospects of these regions separately, focusing on signatures that can appear in lepton flavor violating decays, indirect and direct searches, and the production of these new particles at collider facilities.
Geodesics of Finsler Hayward black hole surrounded by quintessence
Authors: Yashwanth B. R. , Narasimhamurthy S. K. , Nekouee Z. , Malligawad Manjunath
Published: December 2024

This research paper delves into examining the Hayward black hole structure surrounded by quintessence within the framework of Finsler geometry. Our focus centers on the Finsler metric tensor development for black holes. This newly derived metric introduces significant deviations from regular black hole metrics found in general relativity due to the Finslerian term

$$\gamma $$

γ

presence, thus shedding fresh insights into the geometry and nature of black holes. Our findings reveal that the metric structure aligns closely with known Riemannian limits, affirming the congeniality of our model with existing theories. Furthermore, we extended our analysis to derive critical mass values and determine the normalization factor for the Hayward black hole within the Finlserian framework. The study encompasses a detailed description of the horizons and extremal conditions of the Hayward black hole surrounded by quintessence and the impact of the Finsler parameter

$$\gamma $$

γ

on them. Specifically, we explore the case where the quintessence state parameter is set to

$$\omega = -2/3$$

ω
=
-
2
/
3

. Our analysis delves into the effective potential, providing insights into null geodesics for various energy levels and examining the behavior of horizons by utilizing the definition of the effective potential. We also discuss the impact of

$$\gamma $$

γ

for the same. We compute and analyze the radius of circular orbits, the period, the instability characteristics of circular orbits, and the force acting on photons with the newly introduced parameter

$$\gamma $$

γ

within the quintessence field. We have thoroughly looked over the obtained results and discussed them. Additionally, we explore the shadow of the black hole in this context. Thereby, the validity and consistency of our Finslerian model are strengthened. In addition to increasing our understanding of black hole physics, this study paves the way for further research in the Finsler geometry domain and its applications in astrophysics.
The Minkowski vacuum of stochastic composite gravity
Authors: Erlich Joshua
Published: December 2024

We present a first analysis of a nonperturbative approach to quantum gravity based on a representation of quantum field theory in terms of stochastic processes. The stochastic description accommodates a physical Lorentz-invariant ultraviolet regulator that provides a novel description of physics at ultra-short distances. In a scalar toy model, we demonstrate the evolution of a generic initial field configuration toward an equilibrium in which the composite spacetime metric fluctuates about a flat spacetime. As a diffeomorphism-invariant theory with locally Lorentz-invariant regulator, fluctuations about the vacuum are expected to give rise to an emergent gravitational interaction consistent with Einstein gravity at long distances. We uncover a formal similarity between regularization by stochastic discreteness and point-splitting regularization in the corresponding quantum field theory. We comment on the signature of the emergent spacetime, possible consequences for the early universe, and the potential for observational and experimental tests of the stochastic origin of quantum field theory and gravitation.
Effect of shear deformation on electronic and optical properties of monolayer WS2-doped Mo atoms
Authors: Wang Ying , Yang Nan , Gao Xuewen , Su Qing , Liu Guili , Zhang Guoying
Published: December 2024

First-principles research has been used to carefully examine the structural stability of the architecture, electronic structure, and optical characteristics of monolayer WS2-doped Mo atoms during shear deformation. Calculations show that the required formation energy gradually increases when shear deformation is increased from 2% to 8%, the bandgap of the system decreases from 1.732[Formula: see text]eV to 0.922[Formula: see text]eV, and the static dielectric function increases from 2.59 to 2.74. The absorption peaks are maximum for all doped systems between 11.5[Formula: see text]eV and 12.5[Formula: see text]eV. The peak absorption of the deformed system is redshifted compared to the original doped system. With increasing shear deformation, the peak energy loss of the system shows a decrease followed by an increase.
PREY–PREDATOR MODEL WITH ALLEE EFFECT INCORPORATING PREY REFUGE WITH HUNTING COOPERATION
Authors: DAS APARNA , MANDAL SATYARAM , ROY SANKAR KUMAR
Published: December 2024

In this paper, we consider the dynamics of a prey–predator model with logistic growth incorporating refuge in the prey and cooperation among predators population. Furthermore, multiplicative Allee effect in the prey growth is added to account from biological and mathematical perspectives. First, the existence and stability of equilibria of the model are discussed. Next, the existence of several kinds of bifurcation is provided and also studied the direction and stability of Hopf bifurcation. In addition, we study the influence of hunting cooperation on the model analytically and numerically, and find that the hunting cooperation cannot only reduce the density of prey population, but also destabilize the system dynamics irrespective of Allee effect. We choose also the impact of refuge on the model numerically, and explore that refuge stabilize the system dynamics. Moreover, the comparison between the dynamics of strong and weak Allee effect is taken into consideration.
ANALYSIS AND DYNAMICS OF CHOLERA EPIDEMIC SYSTEM IN SOCIETY VIA FRACTAL-FRACTIONAL OPERATOR
Authors: ABBAS FAKHAR , GHAFFAR ABDUL , AKGÜL ALI , AHMAD AQEEL , MUSTAFA GHULAM , HENDY A. S. , ABDALLAH SUHAD ALI OSMAN , ABD EL-GAWAAD N. S.
Published: December 2024

To comprehend the dynamics of disease propagation within a society, mathematical formulation is a crucial tool to understand the complex dynamics. In order to transform the mathematical model with the objective of bolstering the immune system into a fractional-order model, we use the definition of Fractal-Fractional with Mittag-Leffler kernel. For an assessment of the stable position of a recently modified system, qualitative as well as quantitative assessments are carried out. We validate the property positivity and reliability of the developed system by evaluating its boundedness and uniqueness, which are important features of an epidemic model. The positive solutions with linear growth have been verified by the global derivative, and the level of effects of different parameters in each sub-section is determined through employing Lipschitz criteria. By employing Lyapunov’s first and second derivatives of the function, the framework is examined on a global scale to evaluate the overall effect with symptomatic and asymptomatic measures. Bifurcation analysis was performed to check the behavior of each sub-compartment under different parameters effects. The Mittag-Leffler kernel is used to obtain a robust solution via Fractal-Fractional operator for continuous monitoring of spread and control of cholera disease under different dimensions. Simulations are carried out to observe both the symptomatic and asymptomatic consequences of cholera globally, also to observe the actual behavior of cholera disease for control measures, and it has been confirmed that those with strong immune systems individuals recover early due to early detection measures. The actual state of cholera disease can be controlled by taking the following measures: early detection of disease for both individuals receiving medication and those who do not require medication because of their robust immune systems. This kind of research will be beneficial in determining how diseases spread and in developing effective control plans based on our validated findings.
Vitamin B12 functionalized with hydroxy-pyrrol-2-one linkers
Authors: Woźny Mateusz , Fresta Monica , Meffert Jan , Madder Annemieke , Gryko Dorota
Published: December 2024

The modification of biomolecules is significant to chemical biology. One of the challenges is improving the trans-membrane transport, and recently vitamin B[Formula: see text] has emerged as a biocompatible transporter that can facilitate the uptake. This study investigates the formation of adducts between vitamin B[Formula: see text] thiolate and 5HP2O linkers (5-hydroxy-1,5-dihydro-2[Formula: see text]-pyrrol-2-ones) as a novel approach to converting native B[Formula: see text] into versatile bioconjugation-ready intermediates. We synthesized two model 5HP2O linkers and optimized the reaction with the readily available and bench-stable isothiouronium salt of vitamin B[Formula: see text] that generates reactive thiolate in situ. The optimal conditions included using a 1:1 mixture of H2O/EtOH or H2O/DMSO as solvents, excess of 5HP2O, and methylamine, at the concentration of 3.5 mM. This work enriches the bioconjugation toolkit and offers new insights into the development of vitamin B[Formula: see text]-containing therapeutics.
Quantitative Measurement of Cyber Resilience: Modeling and Experimentation
Authors: Weisman Michael J. , Kott Alexander , Ellis Jason E. , Murphy Brian J. , Parker Travis W. , Smith Sidney , Vandekerckhove Joachim
Published: December 2024

Cyber resilience is the ability of a system to resist and recover from a cyber attack, thereby restoring the system’s functionality. Effective design and development of a cyber resilient system requires experimental methods and tools for quantitative measuring of cyber resilience. This article describes an experimental method and test bed for obtaining resilience-relevant data as a system (in our case—a truck) traverses its route, in repeatable, systematic experiments. We model a truck equipped with an autonomous cyber-defense system and which also includes inherent physical resilience features. When attacked by malware, this ensemble of cyber-physical features (i.e., “bonware”) strives to resist and recover from the performance degradation caused by the malware’s attack. We propose parsimonious mathematical models to aid in quantifying systems’ resilience to cyber attacks. Using the models, we identify quantitative characteristics obtainable from experimental data and show that these characteristics can serve as useful quantitative measures of cyber resilience.
PREFER: A Pre-trained Model Recommendation Framework for Edge Computing Enabled Traffic Flow Prediction
Authors: Cai Qiqi , Cao Jian , Chen Yirong , Qian Shiyou , Yuan Liangxiao , Wang Jie
Published: December 2024

The recent years have witnessed a surge in the development of traffic flow prediction methods, often deployed on cloud platforms to offer predictive services for entire transportation networks. However, the processes of training and executing a model for the entire traffic network are both time-consuming and computationally expensive. As a result, the utilization of edge servers for local sub-network prediction services has gained prominence. Nevertheless, training prediction models for numerous sub-networks within the extensive traffic network remains a time-intensive and computing resource-consuming task. To tackle this challenge, this article introduces the Pre-trained model REcommendation Framework for Edge computing enabled tRaffic flow prediction (PREFER). PREFER trains a set of traffic flow prediction models on selected sub-networks, then recommends optimal pre-trained models for edge servers. The recommendation is specifically based on performance prediction, integrating neural collaborative filtering and traffic flow characteristics. Experiments conducted on real datasets reveal that the pre-trained models recommended by PREFER perform close to the actual optimal ones and significantly outperform existing recommendation algorithms.
Margin-aware Noise-robust Contrastive Learning for Partially View-aligned Problem
Authors: Qin Yalan , Pu Nan , Wu Hanzhou , Sebe Nicu
Published: December 2024

In this article, we study a challenging problem in contrastive learning when just a portion of data is aligned in multi-view dataset due to temporal, spatial, or spatio-temporal asynchronism across views. It is important to study partially view-aligned data since this type of data is common in real-world application and easily leads to data inconsistency among different views. Such a Partially View-aligned Problem (PVP) in contrastive learning has been relatively less touched so far, especially in downstream tasks, i.e., classification and clustering. In order to solve this problem, we introduce a flexible margin and propose margin-aware noise-robust contrastive learning to simultaneously identify the within-category counterparts from the other view of one data point based on the established cross-view correspondence and learn a shared representation. To be specific, the proposed learning framework is built on a novel margin-aware noise-robust contrastive loss. Since data pairs are used as input for the proposed margin-aware noise-robust contrastive learning, we build positive pairs according to the known correspondences and negative pairs in the manner of random sampling. Our margin-aware noise-robust contrastive learning framework is able to effectively reduce or remove the impacts caused by the possible existing noise for the constructed pairs in a margin-aware manner, i.e., false negative pairs led by random sampling in PVP. We relax the proposed margin-aware noise-robust contrastive loss and then give a detailed mathematical analysis for the effectiveness of our loss. As an instantiation, we construct an example under the proposed margin-aware noise-robust contrastive learning framework for validation in this work. To the best of our knowledge, this is the first attempt of extending contrastive learning to a margin-aware noise-robust version for dealing with PVP. We also enrich the learning paradigm when there is noise in the data. Extensive experiments on different datasets demonstrate the promising performance of the proposed method in the classification and clustering tasks.
Miniaturize the Redox Flow Battery for Accelerated Materials Discovery and Development
Authors: Feng Ruozhu , Liyu Andrey V. , Kim Soowhan , Zeng Chao , Bracken Carter C. , Liang Yangang , Wang Wei
Published: December 2024

Redox flow batteries are a promising technology for grid-scale energy storage. The aqueous organic redox flow battery is of particular interest for its potentially low material cost and sustainability. Developing novel organic active material for flow battery electrolytes typically entails molecular engineering toward desired properties, necessitating organic synthesis. In a research laboratory setting, the synthesis of specifically designed organic molecules featuring targeted functional groups is time and resources intensive. In the past, synthesizing materials required for battery testing has often required gram-scale production, presenting considerable constraints on the pace of novel organic material discovery. In this report, we introduce a miniaturized cell design that mandates only milligram-scale material synthesis while yielding testing outcomes equivalent or superior to those reported with other commercially available or homemade flow cells in the literature. The test results under various pH conditions validate the scale-down strategy to accelerate the flow battery material discovery and development using the newly designed mini cell. This approach offers researchers an efficient means to notably reduce the time and resources required to develop novel materials for flow batteries.
Restructuring of Sodium-Lead Alloys during Charge-Discharge Cycling in Sodium-Ion Batteries
Authors: Garayt Matthew D. L. , Obialor Martins C. , Monchesky Ian L. , George Andrew E. , Yu Svena , Rutherford Bailey A. , Metzger Michael , Dahn J. R.
Published: December 2024

Sodium-ion batteries (NIBs) are of growing interest due to their expected lower cost than many lithium-ion batteries (LIBs). However, most NIBs suffer from lower volumetric energy density than LIBs. Lead (Pb) can replace hard carbon in the NIB negative electrode to substantially increase its volumetric energy density and has been shown to have no capacity fade over hundreds of cycles in half cells. Pb also experiences 387% volume expansion upon full sodiation, which presumably leads to significant changes in the electrode morphology. In this work, the morphology of Pb and Pb-hard carbon blended electrodes is tracked using scanning electron microscopy. As well, each Na-Pb phase is examined to analyze their physical properties. These analyses show that the Pb particles restructure into ∼1 μm particles, even after just a single cycle, and surprisingly do not pulverize the hard carbon in a blended electrode. Importantly, single-walled carbon nanotubes appear to be necessary to maintain active material electrical connection during the restructuring.
Effect of Annealing Temperatures on Structural and Electrochemical Properties of Li[Ni0.5Co0.25Mn0.25]O2 Film Cathodes
Authors: G Prathibha , Mettu Maheshwar Reddy , Ravindar Reddy M. , Kuntigorla Manjula , Obili Mahammad Hussain
Published: December 2024

Thin films of Li[Ni0.5Co0.25Mn0.25]O2 were prepared by RF-sputtering technique post-annealed the deposited films at various temperatures in a controlled oxygen atmosphere. The annealing temperature played an important role in the crystallinity of the films. The films post-annealed at optimized temperature displayed an X-ray diffraction peak at 18.29°, which can be ascribed to the Braggs reflection (003) of hexagonal Li[Ni0.5Co0.25Mn0.25]O2. The lattice parameters of the optimized films were a = 2.85 Å and c = 14.45 Å with c/a ratio equal to 5.070. The electrochemical activity of the post-annealed films was methodically investigated. The discharge capacity offered by the films is 40 μAh/cm2μm at 300 °C however this was further improved to 57.5 μAh/cm2.μm by post-annealing at 700 °C. Due to structural integrity of Li[Ni0.5Co0.25Mn0.25]O2 film may be used as cathode material for energy storage devices.
Light- and Elevated Temperature-Induced Degradation and Recovery from Silicon Wafers by the Impact of Hydrogen Treatment
Authors: Yousuf Hasnain , Cha Yewon , Jony Jaljalalul Abedin , Zahid Muhammad Aleem , Madara Polgampola Chamani , Khokhar Muhammad Quddamah , Kim Youngkuk , Yi Junsin
Published: December 2024

Light- and elevated-temperature-induced degradation (LeTID) affects materials used in solar cell fabrication, especially gallium- and boron-doped p-type, and various n-type silicon wafers. Dark annealing at elevated temperatures promotes hydrogen diffusion into the bulk of silicon wafers. Here, dark-annealing was consistently performed at 200 °C for 15 min to observe its impact on degradation and recovery. Higher temperatures accelerated LeTID, necessitating rapid annealing for regeneration. The chosen temperature range (75, 120, and 135 °C) was selected to simulate real-world solar panel operating conditions and to observe degradation under both moderate and extreme temperatures. Forming-gas annealing increased the carrier lifetime of boron-doped silicon wafers by up to 92.8% and gallium-doped wafers by up to 16.3% from their initial values after degradation. Dark-annealing resulted in 40% and 28% increases in the carrier lifetimes of fully degraded gallium- and boron-doped silicon wafers, respectively. The proposed model explains the behavior related to different diffusivities of hydrogen in gallium- and boron-doped silicon wafers during dark-annealing. The LeTID mechanism involves three stages: generating inactive recombination centers (Di) and H+ ions during manufacturing, converting Di to HDi+1, enhancing carrier recombination, and, during regeneration, the injection of carriers (e−) transitions to a recombination inactive state.
Correlation between Electrochemical Relaxations and Morphologies of Conducting Polymer Dendrites
Authors: Baron Antoine , Balaguera Enrique H. , Pecqueur Sébastien
Published: December 2024

Conducting Polymer Dendrites (CPD) can engrave sophisticated patterns of electrical interconnects in their morphology with low-voltage spikes and few resources: they may unlock in operando manufacturing functionalities for electronics using metamorphism conjointly with electron transport as part of the information processing. The relationship between structure and information transport remains unclear and hinders the exploitation of the versatility of their morphologies to store and process electrodynamic information. This study details the evolution of CPD's circuit parameters with their growth and shape. Through electrochemical impedance spectroscopy, multiple distributions of relaxation times are evidenced and evolve specifically upon growth. Correlations are established between dispersive capacitances of dendritic morphologies and growth duration, independently from exogenous physical variables: distance, evaporation or aging. Deviation of the anomalous capacitance from the conventional Debye dielectric relaxation can be programmed, as the growth controls the dispersion coefficient of the dendrite's constant-phase elements relaxation. These results suggest that the fading-memory time window of pseudo-capacitive interconnects can practically be conditioned using CPD morphogenesis as an in materio learning mechanism. This study confirms the perspective of using electrochemistry for unconventional electronics, engraving information in the physics of conducting polymer objects, and storing information in their morphology, accessible by impedance spectral analysis.
Placental extracellular vesicles from women with severe preeclampsia alter calcium homeostasis in cardiomyocytes: an ex vivo study
Authors: Murugesan Saravanakumar , Saravanakumar Lakshmi , Sadayappan Sakthivel , Kannappan Ramaswamy , Sinkey Rachel G. , Tubinis Michelle D. , Tita Alan N. , Jilling Tamas , Berkowitz Dan E.
Published: December 2024

This study unveils a novel link between the placenta and PE-linked heart dysfunction. We isolated and characterized placental EVs from pregnancies with sPE and normotensive controls. These plasma sPE-EVs, and sPE-Plex EVs disrupt calcium signaling in heart cells, potentially via reduced STIM1 and PLN proteins. This suggests both plasma sPE-EVs and sPE-Plex EVs cargo drive these disruptive effects. Identifying these cargo molecules (miRNAs or proteins) holds promise for new PE therapies targeting cardiac dysfunction.
Focal adhesions, reticular adhesions, flat clathrin lattices: what divides them, what unites them?
Authors: Lukas Fabian , Duchmann Marlen , Maritzen Tanja
Published: December 2024

The majority of cells within multicellular organisms requires anchorage to their surroundings in the form of cell-cell or cell-matrix adhesions. In regards to cell-matrix adhesions, the transmembrane receptors of the integrin family have long been recognized as the central scaffold around which these adhesion complexes are built. Via their extracellular domains integrins bind extracellular matrix ligands while their intracellular tails interact with a plethora of proteins that link integrin-based adhesions to the cytoskeleton and turn them also into important signaling platforms. Depending on the specific intracellular interactome of the integrins, different types of integrin adhesion complexes have been classified. The best-studied ones are the focal adhesions, in which integrins become firmly linked to contractile actomyosin fibers, allowing force transduction. But integrins also form an integral part of adhesion structures that lack the strong actomyosin link and are enriched in endocytic proteins. These have been named reticular adhesions, flat clathrin lattices, or clathrin plaques. Initially, the different types of integrin adhesion complexes have been viewed as discrete entities with their own separate life cycles. However, in the past years it has become more and more apparent how closely intertwined they are. In fact, it was shown that they can trigger each other’s biogenesis or can even directly convert into each other. Here, we describe similarities as well as differences between integrin adhesion complexes, focusing on the versatile αvβ5 integrins, and discuss the recently discovered close links and interconversion modes between the different αvβ5 integrin adhesion types.
Lactobacillus reuteri Alleviates Hyperoxia‐Induced BPD by Activating IL‐22/STAT3 Signaling Pathway in Neonatal Mice
Authors: Zhang Meiyu , Li Decai , Sun Liujuan , He Yu , Liu Qingqing , He Yi , Li Fang
Published: December 2024

Bronchopulmonary dysplasia (BPD) is the most common chronic respiratory disease in preterm infants. Little is known about the regulatory effect of lung Lactobacillus and its mechanism in BPD. This study explored the effect of L. reuteri on hyperoxia‐induced mice lung injuries and examined whether L. reuteri played a role via the IL‐22/STAT3 pathway. We found that the intranasal administration of L. reuteri and its tryptophan metabolite indole‐3‐aldehyde (3‐IAld) ameliorated hyperoxia‐induced mice lung BPD‐like changes, deceased proinflammatory cytokines (IL‐1β, IL‐6, and TNF‐α), and increased the levels of surfactant‐associated protein C (SPC), aquaporin 5 (AQP5), and vascular endothelial growth factor receptor 2 (VEGFR2, also known as FLK‐1). Furthermore, L. reuteri and 3‐IAld increased the expression of IL‐22. IL‐22 was also confirmed to ameliorate hyperoxia‐induced mice lung pathological changes, and the protective effects of L. reuteri could be inhibited by anti‐IL‐22 neutralizing antibody. Finally, we confirmed STAT3 activation by IL‐22 in MLE‐12 cells. In summary, our study confirmed L. reuteri alleviated hyperoxia‐induced lung BPD‐like changes in mice by activating the IL‐22/STAT3 signaling pathway via IL‐22 production. Probiotics Lactobacillus is a potential treatment for hyperoxia‐induced lung injury in newborns.
Antimycobacterial and Antifungal Activities of Leaf Extracts From Trichilia emetica
Authors: Mugayi Lydia Chenesai , Mukanganyama Stanley
Published: December 2024

The global problem of infectious and deadly diseases caused by microbes such as candida and mycobacteria presents major scientific and medical challenges. Antimicrobial drug resistance is a rapidly growing problem with potentially devastating consequences. Various pathogens can cause skin infections, such as bacteria, fungi, and parasites. Antimicrobial resistance has caused the urgency to seek alternative treatment options from available natural resources. Plant‐derived medicinal compounds can provide novel alternative treatment avenues against pathogenic microbes. The objective of this study was to determine the antimycobacterial and antifungal activity of leaf extracts of Trichilia emetica against Mycobacteria smegmatis, Mycobacteria aurum, Candida tropicalis, and Candida albicans. The leaf extracts were prepared using hexane, ethyl acetate, acetone, dichloromethane (DCM), methanol, ethanol, water, DCM:methanol, and 70% ethanolic aqueous solution. The microbroth dilution was used to determine the minimum inhibitory concentration (MIC) of each extract against the four test organisms. The mode of action by which these extracts inhibit growth was also investigated. The effects of the extract on the cell wall of C. tropicalis were determined using the sorbitol assay. The effects of the extracts on the membrane integrity of the test organisms were determined using propidium iodide, which binds to nucleic acids, and the Bradford reagent, which reacts with proteins. The ethyl acetate and 70% ethanolic aqueous extracts were most potent against the organisms tested with MICs ranging from 125 to 1000 μg/mL. However, the two extracts did not inhibit the growth of C. tropicalis in the presence of sorbitol. The extracts caused the leakage of nucleic acids and proteins in C. tropicalis and M. smegmatis only and not in M. aurum. It is concluded that the leaf extracts of T. emetica have antimycobacterial or antifungal activities. The disruption of cell membranes resulting in protein and nucleic acid leakage could be the plant’s possible mode of action.