bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Basis of the Curative Effects of Turkish Gall Extracts on Periodontitis
Authors: Luo Xiaojie , Zha Siqin , Su Xu , Wang Yue , Zhang Miao , Chen Xiaotao 
Published: April 2024

AbstractWe explored the mechanism whereby Turkish gall extracts prevent and effectively cure periodontitis. Main bioactive components were obtained from previous reports and targets were screened using TCMSP, PubChem, SwissTargetPrediction, and Drugbank databases. Chronic periodontitis targets were retrieved from OMIM, GeneCards, and DisGeNET databases. Intersectional targets of Turkish galls and periodontitis were obtained using Venn analysis. String databases were used to construct a protein–protein interaction network of common targets. R language was used for GO and KEGG enrichment analyses of common targets. Molecular docking analysis confirmed Turkish gall extract effectiveness for periodontitis treatment, which was verified in vitro and inhibited MAPK1, MAPK3 and SRC expression. We predicted 759 possible target genes. Among 2059 identified periodontitis genes, 205 overlapped with those in methanolic Turkish gall extract. Key targets included JUN, tumor protein 53, MAPK1, MAPK3, STAT3, RELA, and SRC. GO analysis showed that common targets were mainly involved in processes such as oxidative stress. KEGG analysis indicated that common targets were enriched in 163 pathways. Molecular docking analysis showed that 1,2,3,6‐tetra‐O‐galloyl‐β‐D‐glucose, 1,3,6‐tri‐O‐galloyl‐β‐D‐glucose and 1,2,3,4,6‐penta‐O‐galloyl‐β‐D‐glucose were strongly associated with MAPK1, MAPK3, and SRC. Turkish gall extract reduced inflammation and targets expression in vitro, providing a reference for drug development for periodontitis.
What next? Some practical suggestions for future studies on fence ecology
Authors: Buton Caryl , Kaldonski Nicolas , Nowicki François , Saint‐Andrieux Christine 
Published: April 2024

Practical gaps in knowledge of fence ecology or its specific requirements still exist despite numerous recommendations scattered throughout various articles. We recently carried out two different studies on fences in a French context whose results corroborate this observation, and highlight the need to synthetise and prioritise scientific and technical research. The first study was an exploratory research project on escape devices used to allow ungulates to exit fenced transport infrastructure right‐of‐way. The second study entailed drafting a guide on the mitigation of the fence's ecological impacts, using solar energy plants as a case study. Both were based on different types of information gathering, ranging from bibliographical research to interviews with governments officials, operating companies, engineering offices, naturalists and hunters' associations.Based on the similarities between these two studies, the urgency of certain needs, and the clear potential for these approaches to extend beyond France's borders, we have identified two key categories for future actions. The first category is a series of six research priorities: Diversifying monitoring of exclusion fencing; Developing practice‐oriented fence mapping tools; Further studying the impact of fencing on animal vehicle collisions; Considering animal behaviour in monitoring protocol; Ex‐situ testing of devices' effectiveness; and Studying large‐scale effects of fencing. The second category comprises six method recommendations: Accurately documenting fences; Early planning of scientific monitoring; Contextualising fencing requirements; Defining effectiveness goals and criteria; Taking advantage of opportunistic Animal‐Fence Event observations; and Developing artificial intelligence and computer vision to map fences. All these items are supported by examples drawn from one study or the other.Our conclusions indicate that, in the context of major expansion of fences, such recommendations must be integrated at all stages of development work. If this is not implemented, the free movement of animal species will not be adequately protected and the erosion of biodiversity will be further exacerbated.
On Basic Feasible Functionals and the Interpretation Method
Authors: Baillot Patrick , Dal Lago Ugo , Kop Cynthia , Vale Deivid 
Published: April 2024

AbstractThe class of basic feasible functionals ($$\texttt{BFF}$$
BFF
) is the analog of $$\texttt{FP}$$
FP
(polynomial time functions) for type-2 functionals, that is, functionals that can take (first-order) functions as arguments. $$\texttt{BFF}$$
BFF
can be defined through Oracle Turing machines with running time bounded by second-order polynomials. On the other hand, higher-order term rewriting provides an elegant formalism for expressing higher-order computation. We address the problem of characterizing $$\texttt{BFF}$$
BFF
by higher-order term rewriting. Various kinds of interpretations for first-order term rewriting have been introduced in the literature for proving termination and characterizing (first-order) complexity classes. In this paper, we consider a recently introduced notion of cost–size interpretations for higher-order term rewriting and see definitions as ways of computing functionals. We then prove that the class of functionals represented by higher-order terms admitting a certain kind of cost–size interpretation is exactly $$\texttt{BFF}$$
BFF
.
Craig Interpolation for Decidable First-Order Fragments
Authors: ten Cate Balder , Comer Jesse 
Published: April 2024

AbstractWe show that the guarded-negation fragment (GNFO) is, in a precise sense, the smallest extension of the guarded fragment (GFO) with Craig interpolation. In contrast, we show that the smallest extension of the two-variable fragment ($$\textrm{FO}^2 $$

FO
2

), and of the forward fragment (FF) with Craig interpolation, is full first-order logic. Similarly, we also show that all extensions of $$\textrm{FO}^2 $$

FO
2

and of the fluted fragment (FL) with Craig interpolation are undecidable.
Towards Reliable SQL Synthesis: Fuzzing-Based Evaluation and Disambiguation
Authors: Brancas Ricardo , Terra-Neves Miguel , Ventura Miguel , Manquinho Vasco , Martins Ruben 
Published: April 2024

AbstractIn recent years, more people have seen their work depend on data manipulation tasks. However, many of these users do not have the background in programming required to write complex programs, particularly SQL queries. One way of helping these users is automatically synthesizing the SQL query given a small set of examples. Several program synthesizers for SQL have been recently proposed, but they do not leverage multicore architectures.This paper proposes Cubes, a parallel program synthesizer for the domain of SQL queries using input-output examples. Since input-output examples are an under-specification of the desired SQL query, sometimes, the synthesized query does not match the user’s intent. Cubes incorporates a new disambiguation procedure based on fuzzing techniques that interacts with the user and increases the confidence that the returned query matches the user intent. We perform an extensive evaluation on around 4000 SQL queries from different domains. Experimental results show that our parallel approach can scale up to 16 processes with super-linear speedups for many hard instances, and that our disambiguation approach is critical to achieving an accuracy of around 60%, significantly larger than other SQL synthesizers.
Probabilistic Runtime Enforcement of Executable BPMN Processes
Authors: Falcone Yliès , Salaün Gwen , Zuo Ahang 
Published: April 2024

AbstractA business process is a collection of structured tasks corresponding to a service or a product. Business processes do not execute once and for all, but are executed multiple times resulting in multiple instances. In this context, it is particularly difficult to ensure correctness and efficiency of the multiple executions of a process. In this paper, we propose to rely on Probabilistic Model Checking (PMC) to automatically verify that multiple executions of a process respect some specific probabilistic property. This approach applies at runtime, thus the evaluation of the property is periodically verified and the corresponding results updated. However, we go beyond runtime PMC for BPMN, since we propose runtime enforcement techniques to keep executing the process while avoiding the violation of the property. To do so, our approach combines monitoring techniques, computation of probabilistic models, PMC, and runtime enforcement techniques. The approach has been implemented as a toolchain and has been validated on several realistic BPMN processes.
Refinement Verification of OS Services based on a Verified Preemptive Microkernel
Authors: Li Ximeng , Chen Shanyan , Guan Yong , Zhang Qianying , Wang Guohui , Shi Zhiping 
Published: April 2024

AbstractAn OS microkernel can be extended by implementing services upon it. A service could introduce an object that references a kernel object, and implement a group of functions that invokes the functions for manipulating the kernel object. We consider the scenario where the microkernel has been verified with machine-checkable proofs, while the services remain to be verified. Moreover, the verification of the microkernel is not performed with the verification of subsequent extension in mind. We address the problem of how to build sufficiently on the verification results for the microkernel, in achieving the verification of the services. Our methodology consists of enhancements to the verification framework for the microkernel, and the design of invariants for establishing the connection between the service-level objects and the kernel-level objects. Using the methodology, we have conducted a substantial formal verification of a group of services extending the inter-task communication functionalities of the preemptive microkernel $$\mu \!\!\text{ C }\!\!\text{/ }\!\!\!\text{ OS-II }$$

μ

C

/

OS-II

. Our verification uncovers dormant bugs and provides a level of correctness assurance for the services that is above what is achievable through extensive testing.
Global centers of a family of cubic systems
Authors: Appis Raul Felipe , Llibre Jaume 
Published: April 2024

AbstractConsider the family of polynomial differential systems of degree 3, or simply cubic systems $$ x' = y, \quad y' = -x + a_1 x^2 + a_2 xy + a_3 y^2 + a_4 x^3 + a_5 x^2 y + a_6 xy^2 + a_7 y^3, $$

x
′

=
y
,

y
′

=
-
x
+

a
1

x
2

+

a
2

x
y
+

a
3

y
2

+

a
4

x
3

+

a
5

x
2

y
+

a
6

x

y
2

+

a
7

y
3

,

in the plane $$\mathbb {R}^2$$

R

2

. An equilibrium point $$(x_0,y_0)$$

(

x
0

,

y
0

)

of a planar differential system is a center if there is a neighborhood $$\mathcal {U}$$
U
of $$(x_0,y_0)$$

(

x
0

,

y
0

)

such that $$\mathcal {U} \backslash \{(x_0,y_0)\}$$

U
\
{

(

x
0

,

y
0

)

}

is filled with periodic orbits. When $$\mathbb {R}^2\setminus \{(x_0,y_0)\}$$

R

2

\

{

(

x
0

,

y
0

)

}

is filled with periodic orbits, then the center is a global center. For this family of cubic systems Lloyd and Pearson characterized in Lloyd and Pearson (Comput Math Appl 60:2797–2805, 2010) when the origin of coordinates is a center. We classify which of these centers are global centers.
CRL4DCAF13 E3 ubiquitin ligase targets MeCP2 for degradation to prevent DNA hypermethylation and ensure normal transcription in growing oocytes
Authors: Ren Peipei , Tong Xiaomei , Li Junjian , Jiang Huifang , Liu Siya , Li Xiang , Lai Mengru , Yang Weijie , Rong Yan , Zhang Yingyi , Jin Jiamin , Ma Yerong , Pan Weiwei , Fan Heng-Yu , Zhang Songying , Zhang Yin-Li 
Published: April 2024

AbstractThe DNA methylation is gradually acquired during oogenesis, a process sustained by successful follicle development. However, the functional roles of methyl-CpG-binding protein 2 (MeCP2), an epigenetic regulator displaying specifical binding with methylated DNA, remains unknown in oogenesis. In this study, we found MeCP2 protein was highly expressed in primordial and primary follicle, but was almost undetectable in secondary follicles. However, in aged ovary, MeCP2 protein is significantly increased in both oocyte and granulosa cells. Overexpression of MeCP2 in growing oocyte caused transcription dysregulation, DNA hypermethylation, and genome instability, ultimately leading to follicle growth arrest and apoptosis. MeCP2 is targeted by DCAF13, a substrate recognition adaptor of the Cullin 4-RING (CRL4) E3 ligase, and polyubiquitinated for degradation in both cells and oocytes. Dcaf13-null oocyte exhibited an accumulation of MeCP2 protein, and the partial rescue of follicle growth arrest induced by Dcaf13 deletion was observed following MeCP2 knockdown. The RNA-seq results revealed that large amounts of genes were regulated by the DCAF13-MeCP2 axis in growing oocytes. Our study demonstrated that CRL4DCAF13 E3 ubiquitin ligase targets MeCP2 for degradation to ensure normal DNA methylome and transcription in growing oocytes. Moreover, in aged ovarian follicles, deceased DCAF13 and DDB1 protein were observed, indicating a potential novel mechanism that regulates ovary aging.
Bilayer surrogate brain response under various blast loading conditions
Authors: Norris C. , Arnold B. , Wilkes J. , Squibb C. , Nelson A. J. , Schwenker H. , Mesisca J. , Vossenberg A. , VandeVord P. J. 
Published: April 2024

AbstractVariations in the experimental constraints applied within blast simulations can result in dramatically different measured biomechanical responses. Ultimately, this limits the comparison of data between research groups and leads to further inquisitions about the “correct” biomechanics experienced in blast environments. A novel bilayer surrogate brain was exposed to blast waves generated from advanced blast simulators (ABSs) where detonation source, boundary conditions, and ABS geometry were varied. The surrogate was comprised of Sylgard 527 (1:1) as a gray matter simulant and Sylgard 527 (1:1.2) as a white matter simulant. The intracranial pressure response of this surrogate brain was measured in the frontal region under primary blast loading while suspended in a polyurethane spherical shell with 5 mm thickness and filled with water to represent the cerebrospinal fluid. Outcomes of this work discuss considerations for future experimental designs and aim to address sources of variability confounding interpretation of biomechanical responses.
The Fourier spectrum and sumset type problems
Authors: Fraser Jonathan M. 
Published: April 2024

AbstractWe introduce and study the Fourier spectrum which is a continuously parametrised family of dimensions living between the Fourier dimension and the Hausdorff dimension for both sets and measures. We establish some fundamental theory and motivate the concept via several applications, especially to sumset type problems. For example, we study dimensions of convolutions and sumsets, and solve the distance set problem for sets satisfying certain Fourier analytic conditions.
Entire solutions with and without radial symmetry in balanced bistable reaction–diffusion equations
Authors: Taniguchi Masaharu 
Published: April 2024

AbstractLet $$n\ge 2$$

n
≥
2

be a given integer. In this paper, we assert that an n-dimensional traveling front converges to an $$(n-1)$$

(
n
-
1
)

-dimensional entire solution as the speed goes to infinity in a balanced bistable reaction–diffusion equation. As the speed of an n-dimensional axially symmetric or asymmetric traveling front goes to infinity, it converges to an $$(n-1)$$

(
n
-
1
)

-dimensional radially symmetric or asymmetric entire solution in a balanced bistable reaction–diffusion equation, respectively. We conjecture that the radially asymmetric entire solutions obtained in this paper are associated with the ancient solutions called the Angenent ovals in the mean curvature flows.
Sense of Place and Perceived Impacts in the Rural Industrialized Nexus: Insights for Sustainability Pathways
Authors: Weeks Deseret , Jenkins Jeffrey 
Published: April 2024

AbstractAs representative of the water-energy-food nexus, fossil fuel development and industrial agriculture are rural industries that continue to expand and increasingly occur in the same areas. Being a top agricultural export county and the fossil fuel capital of California while ranking among the worst in the US for industrial pollution, Kern County is a poster child of rural nexus development and, thus, an essential place for initiating sustainability transitions. Such transitions rely on policy support and the adoption of methods by individuals and communities who may disagree with such changes. While sense of place and impact perceptions are recognized as playing critical roles in sustainability management, they have yet to be utilized in nexus research. A survey (N = 256) of the perceived impacts of nexus industries with place meaning and place attachment as possible drivers for perceptions was conducted in nexus industry pollution exposure risk zones. Factor analysis and bivariate correlations showed that place meaning and place attachment are drivers for perceptions while also being drivers for concern for changes in nexus industries. While perceptions of impacts indicated contested place meanings, participants strongly perceive the economy and environment as being in decline. To build support for sustainability policy, directing funds from Kern County’s renewable energy industry to local sectors of society, implementation of regenerative agriculture, cooperative management, and nurturing place meaning as aligned with nature’s restorative quality are important paths forward. These nexus management foci could strengthen place attachment, build trust in government, and repair environmental alienation.
Water and carbon footprints in irrigated vineyards: an on-farm assessment
Authors: Tomaz Alexandra , Dôres José , Martins Inês , Catarino Adriana , Boteta Luís , Santos Marta , Patanita Manuel , Palma Patrícia 
Published: April 2024

AbstractThis research aims to contribute to improving water and carbon efficiency in irrigated grapevine production in the dry Mediterranean climate of southern Europe. In regions with water scarcity, irrigation has become a relevant input in viticulture, essential to increase productivity and achieve profits. The joint estimation of the water footprint (WF) and the carbon footprint (CF) can help to comprehensively assess the environmental implications and sustainability associated with water-intensive grapevine cultivation. In this study, the WF and CF, of the farming stage of grapes production, were calculated for three years, in three vineyards located in southern Portugal. Data used for the calculation included meteorological data, irrigation requirements, energy use, fertilizers, and pesticide inputs. The total WF mean value for the study period was 223 m3 ton−1, lower than values found for similar conditions, but the blue component, related to irrigation, was predominant, with a higher proportion (75%) occurring during the driest year. The mean total CF was 98 kg CO2e ton−1; the major contributors were fuel use, fertilizer greenhouse gas emissions, and energy for irrigation. The factor analysis revealed relationships between footprint components, yielding latent variables participated by irrigation water and energy use, pollution loads and agrichemicals use. The examination of trade-offs and/or advantageous relations between footprints and yields showed that seasonal climate conditions play an important role via their effect on the farming practices and the inputs most influential on these indicators, namely: crop water requirement; irrigation volumes; energy for irrigation; fuel consumption; nitrogen and phosphorus fertilization rates.
Memory effects in disease modelling through kernel estimates with oscillatory time history
Authors: Mielke Adam , Sørensen Mads Peter , Wyller John 
Published: April 2024

AbstractWe design a linear chain trick algorithm for dynamical systems for which we have oscillatory time histories in the distributed time delay. We make use of this algorithmic framework to analyse memory effects in disease evolution in a population. The modelling is based on a susceptible-infected-recovered SIR—model and on a susceptible-exposed-infected-recovered SEIR—model through a kernel that dampens the activity based on the recent history of infectious individuals. This corresponds to adaptive behavior in the population or through governmental non-pharmaceutical interventions. We use the linear chain trick to show that such a model may be written in a Markovian way, and we analyze the stability of the system. We find that the adaptive behavior gives rise to either a stable equilibrium point or a stable limit cycle for a close to constant number of susceptibles, i.e. locally in time. We also show that the attack rate for this model is lower than it would be without the dampening, although the adaptive behavior disappears as time goes to infinity and the number of infected goes to zero.
Borrelia burgdorferi and autoimmune mechanisms: implications for mimicry, misdiagnosis, and mismanagement in Lyme disease and autoimmune disorders
Authors: Doskaliuk Bohdana , Zimba Olena 
Published: April 2024

AbstractThe genus Borrelia encompasses a diverse group of spirochetes transmitted primarily by ticks, with Borrelia burgdorferi causing Lyme disease, which is prevalent in North America and Europe. Borrelia’s structural adaptations and ability to persist in diverse host tissues underscore its pathogenic potential. Beyond traditional infectious responses, Borrelia engages in complex interactions with the host immune system, contributing to autoimmune mechanisms such as molecular mimicry and persistent infections. This intricate interplay manifests in symptoms resembling various autoimmune diseases, including systemic lupus erythematosus, dermatomyositis, local scleroderma, and systemic sclerosis. However, these associations lack a precise explanation, emphasizing the need for further investigation. The cases of misdiagnosis between Lyme borreliosis and autoimmune diseases highlight the critical importance of accurate diagnostics and adherence to guidelines. Understanding Borrelia’s impact on immune responses is pivotal for advancing diagnostics and targeted therapeutic interventions in Lyme borreliosis and its potential autoimmune implications.
The combined influence of spin and roughness frequency on sphere aerodynamics
Authors: Elliott Jack , Smith Lloyd , Lyu Bin , Smith Barton L. 
Published: April 2024

AbstractThe lift and drag of spinning spheres roughened with macro-roughness elements are examined. The velocity field of these same spheres in flight is measured with particle image velocimetry (PIV). Several spheres with varying roughness are examined at various spin rates and fixed Reynolds number. Unlike previous studies, where the roughness height is varied, in the present work, the number of roughness elements is varied. The PIV datasets are used to determine the boundary layer separation points for each case. Comparing the lift and drag to the separation points reveals that (1) the separation points become more asymmetric with spin (the Magnus effect), (2) The drag increases with the size of the wake, and (3) the drag increases with the asymmetry of the separation points, meaning that lift on spheres is accompanied by increased drag. Scant evidence of this third effect has been reported previously. Additionally, it is shown that, counter to smooth spheres, the force transmitted to the surface through the roughness elements leads to significant drag. The drag is shown to increase with the number of roughness elements while the lift decreases. Results have implications for understanding aerodynamic forces on bluff bodies with roughness and passive control of aerodynamic forces through roughness element frequency rather than the traditional roughness height.
On the Edge-Erdős–Pósa Property of Ladders
Authors: Steck Raphael , Ulmer Arthur 
Published: April 2024

AbstractWe prove that the ladder with 3 rungs and the house graph have the edge-Erdős–Pósa property, while ladders with 14 rungs or more have not. Additionally, we prove that the latter bound is optimal in the sense that the only known counterexample graph does not permit a better result.