bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the role of FAT genes in Solanaceae species through genome‐wide analysis and genome editing
Authors: Bahadır Sibel , Abdulla Mohamed Farah , Mostafa Karam , Kavas Musa , Hacıkamiloğlu Safa , Kurt Orhan , Yıldırım Kubilay 
Published: September 2024

AbstractPlants produce numerous fatty acid derivatives, and some of these compounds have significant regulatory functions, such as governing effector‐induced resistance, systemic resistance, and other defense pathways. This study systematically identified and characterized eight FAT genes (Acyl‐acyl carrier protein thioesterases), four in the Solanum lycopersicum and four in the Solanum tuberosum genome. Phylogenetic analysis classified these genes into four distinct groups, exhibiting conserved domain structures across different plant species. Promoter analysis revealed various cis‐acting elements, most of which are associated with stress responsiveness and growth and development. Micro‐RNA (miRNA) analysis identified specific miRNAs, notably miRNA166, targeting different FAT genes in both species. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein 9 (CRISPR/Cas9)‐mediated knockout, mutant lines for SlFATB1 and SlFATB3 were successfully generated and exhibited diverse mutation types. Biochemical evaluation of selected mutant lines revealed significant changes in fatty acid composition, with linoleic and linolenic acid content variations. The study also explored the impact of FAT gene knockout on tomato leaf architecture through scanning electron microscopy, providing insights into potential morphological alterations. Knocking out of FAT genes resulted in a significant reduction in both trichome and stoma density. These findings contribute to a comprehensive understanding of FAT genes in Solanaceous species, encompassing genetic, functional, and phenotypic aspects.
Partially Observable Stochastic Games with Neural Perception Mechanisms
Authors: Yan Rui , Santos Gabriel , Norman Gethin , Parker David , Kwiatkowska Marta 
Published: September 2024

AbstractStochastic games are a well established model for multi-agent sequential decision making under uncertainty. In practical applications, though, agents often have only partial observability of their environment. Furthermore, agents increasingly perceive their environment using data-driven approaches such as neural networks trained on continuous data. We propose the model of neuro-symbolic partially-observable stochastic games (NS-POSGs), a variant of continuous-space concurrent stochastic games that explicitly incorporates neural perception mechanisms. We focus on a one-sided setting with a partially-informed agent using discrete, data-driven observations and another, fully-informed agent. We present a new method, called one-sided NS-HSVI, for approximate solution of one-sided NS-POSGs, which exploits the piecewise constant structure of the model. Using neural network pre-image analysis to construct finite polyhedral representations and particle-based representations for beliefs, we implement our approach and illustrate its practical applicability to the analysis of pedestrian-vehicle and pursuit-evasion scenarios.
cfaults: Model-Based Diagnosis for Fault Localization in C with Multiple Test Cases
Authors: Orvalho Pedro , Janota Mikoláš , Manquinho Vasco 
Published: September 2024

AbstractDebugging is one of the most time-consuming and expensive tasks in software development. Several formula-based fault localization (FBFL) methods have been proposed, but they fail to guarantee a set of diagnoses across all failing tests or may produce redundant diagnoses that are not subset-minimal, particularly for programs with multiple faults.This paper introduces a novel fault localization approach for C programs with multiple faults. CFaults leverages Model-Based Diagnosis (MBD) with multiple observations and aggregates all failing test cases into a unified MaxSAT formula. Consequently, our method guarantees consistency across observations and simplifies the fault localization procedure. Experimental results on two benchmark sets of C programs, TCAS and C-Pack-IPAs, show that CFaults is faster than other FBFL approaches like BugAssist and SNIPER. Moreover, CFaults only generates subset-minimal diagnoses of faulty statements, whereas the other approaches tend to enumerate redundant diagnoses.
Unifying Weak Memory Verification Using Potentials
Authors: Bargmann Lara , Dongol Brijesh , Wehrheim Heike 
Published: September 2024

AbstractConcurrency verification for weak memory models is inherently complex. Several deductive techniques based on proof calculi have recently been developed, but these are typically tailored towards a single memory model through specialised assertions and associated proof rules. In this paper, we propose an extension to the logic $${\textsf{Piccolo}}$$
Piccolo
to generalise reasoning across different memory models. $${\textsf{Piccolo}}$$
Piccolo
is interpreted on the semantic domain of thread potentials. By deriving potentials from weak memory model states, we can define the validity of $${\textsf{Piccolo}}$$
Piccolo
formulae for multiple memory models. We moreover propose unified proof rules for verification on top of $${\textsf{Piccolo}}$$
Piccolo
. Once (a set of) such rules has been shown to be sound with respect to a memory model $${\textsf{MM}} $$
MM
, all correctness proofs employing this rule set are valid for $${\textsf{MM}}$$
MM
. We exemplify our approach on the memory models $${\textsf{SC}}$$
SC
, $${\textsf{TSO}}$$
TSO
and $${\textsf{SRA}}$$
SRA
using the standard litmus tests Message-Passing and IRIW.
Sound and Complete Witnesses for Template-Based Verification of LTL Properties on Polynomial Programs
Authors: Chatterjee Krishnendu , Goharshady Amir , Goharshady Ehsan , Karrabi Mehrdad , Žikelić Đorđe 
Published: September 2024

AbstractWe study the classical problem of verifying programs with respect to formal specifications given in the linear temporal logic (LTL). We first present novel sound and complete witnesses for LTL verification over imperative programs. Our witnesses are applicable to both verification (proving) and refutation (finding bugs) settings. We then consider LTL formulas in which atomic propositions can be polynomial constraints and turn our focus to polynomial arithmetic programs, i.e. programs in which every assignment and guard consists only of polynomial expressions. For this setting, we provide an efficient algorithm to automatically synthesize such LTL witnesses. Our synthesis procedure is both sound and semi-complete. Finally, we present experimental results demonstrating the effectiveness of our approach and that it can handle programs which were beyond the reach of previous state-of-the-art tools.
The Opacity of Timed Automata
Authors: An Jie , Gao Qiang , Wang Lingtai , Zhan Naijun , Hasuo Ichiro 
Published: September 2024

AbstractOpacity serves as a critical security and confidentiality property, which concerns whether an intruder can unveil a system’s secret based on structural knowledge and observed behaviors. Opacity in timed systems presents greater complexity compared to untimed systems, and it has been established that opacity for timed automata is undecidable. However, the original proof cannot be applied to decide the opacity of one-clock timed automata directly. In this paper, we explore three types of opacity within timed automata: language-based timed opacity, initial-location timed opacity, and current-location timed opacity. We begin by formalizing these concepts and establishing transformation relations among them. Subsequently, we demonstrate the undecidability of the opacity problem for one-clock timed automata. Furthermore, we offer a constructive proof for the conjecture regarding the decidability of opacity for timed automata in discrete-time semantics. Additionally, we present a sufficient condition and a necessary condition for the decidability of opacity in specific subclasses of timed automata.
A Divide-and-Conquer Approach to Variable Elimination in Linear Real Arithmetic
Authors: Promies Valentin , Ábrahám Erika 
Published: September 2024

AbstractWe introduce a novel variable elimination method for conjunctions of linear real arithmetic constraints. In prior work, we derived a variant of the Fourier-Motzkin elimination, which uses case splitting to reduce the procedure’s complexity from doubly to singly exponential. This variant, which we call FMplex, was originally developed for satisfiability checking, and it essentially performs a depth-first search in a tree of sub-problems. It can be adapted straightforwardly for the task of quantifier elimination, but it returns disjunctions of conjunctions, even though the solution space can always be defined by a single conjunction. Our main contribution is to show how to efficiently extract an equivalent conjunction from the search tree. Besides the theoretical foundations, we explain how the procedure relates to other methods for quantifier elimination and polyhedron projection. An experimental evaluation demonstrates that our implementation is competitive with established tools.
Free Facts: An Alternative to Inefficient Axioms in Dafny
Authors: Bordis Tabea , Leino K. Rustan M. 
Published: September 2024

AbstractFormal software verification relies on properties of functions and built-in operators. Unless these properties are handled directly by decision procedures, an automated verifier includes them in verification conditions by supplying them as universally quantified axioms or theorems. The use of quantifiers sometimes leads to bad performance, especially if automation causes the quantifiers to be instantiated many times.This paper proposes free facts as an alternative to some axioms. A free fact is a pre-instantiated axiom that is generated alongside the formulas in a verification condition that can benefit from the facts. Replacing an axiom with free facts thus reduces the number of quantifiers in verification conditions. Free facts are statically triggered by syntactic occurrences of certain patterns in the proof terms. This is less powerful than the dynamically triggered patterns used during proof construction. However, the paper shows that free facts perform well in practice.
The shape of non-graviton operators for SU(2)
Authors: Choi Sunjin , Kim Seok , Lee Eunwoo , Park Jaemo 
Published: September 2024

Abstract
The BPS spectrum of AdS/CFT exhibits multi-gravitons at low energies, while having black hole states at higher energies. This can be studied concretely in AdS5/CFT4 in terms of classical cohomologies, even in the quantum regimes at finite 1/N. Recently, Chang and Lin found a threshold for non-graviton states in the SU(2) maximal super-Yang-Mills theory. We explicitly construct and present this threshold cohomology.
Helicity evolution at small x: quark to gluon and gluon to quark transition operators
Authors: Borden Jeremy , Kovchegov Yuri V. , Li Ming 
Published: September 2024

Abstract
We include the quark to gluon and gluon to quark shock-wave transition operators into the small Bjorken-x evolution equations for helicity in the flavor-singlet channel derived earlier in [1–3]. While such transitions do not affect the large-Nc version of the evolution equations for helicity, the large-Nc & Nf equations are affected. (Nc and Nf are the numbers of quark colors and flavors, respectively.) We derive the corresponding corrected large-Nc & Nf equations for the polarized dipole amplitudes contributing to the flavor-singlet quark and gluon helicity distributions in the double-logarithmic approximation (DLA), resumming powers of αs ln2(1/x) with αs the strong coupling constant. We solve these equations iteratively and extract the polarized splitting functions up to four loops. We show that our splitting functions agree with the fixed-order perturbative calculations up to and including the existing three-loops results [4–7]. Similar to the large-Nc helicity evolution in the shock-wave approach [8], our large-Nc & Nf small-x splitting functions agree with those obtained in the infrared evolution equations framework from [9, 10] up to three loops, but appear to slightly disagree at four loops.
Analyticity and the Unruh effect: a study of local modular flow
Authors: Sorce Jonathan 
Published: September 2024

Abstract
The Unruh effect can be formulated as the statement that the Minkowski vacuum in a Rindler wedge has a boost as its modular flow. In recent years, other examples of states with geometrically local modular flow have played important roles in understanding energy and entropy in quantum field theory and quantum gravity. Here I initiate a general study of the settings in which geometric modular flow can arise, showing (i) that any geometric modular flow must be a conformal symmetry of the background spacetime, and (ii) that in a well behaved class of “weakly analytic” states, geometric modular flow must be future-directed. I further argue that if a geometric transformation is conformal but not isometric, then it can only be realized as modular flow in a conformal field theory. Finally, I discuss a few settings in which converse results can be shown — i.e., settings in which a state can be constructed whose modular flow reproduces a given vector field.
Sterile neutrino dark matter within the νSMEFT
Authors: Fuyuto Kaori , Kumar Jacky , Mereghetti Emanuele , Sandner Stefan , Sun Chen 
Published: September 2024

Abstract
Sterile neutrinos with masses at the keV scale and mixing to the active neutrinos offer an elegant explanation of the observed dark matter (DM) density. However, the very same mixing inevitably leads to radiative photon emission and the non-observation of such peaked X-ray lines rules out this minimal sterile neutrino DM hypothesis. We show that in the context of the Standard Model effective field theory with sterile neutrinos (νSMEFT), higher dimensional operators can produce sterile neutrino DM in a broad range of parameter space. In particular, νSMEFT interactions can open the large mixing parameter space due to their destructive interference, through operator mixing or matching, in the X-ray emission. We also find that, even in the zero mixing limit, the DM density can always be explained by νSMEFT operators. The testability of the studied νSMEFT operators in searches for electric dipole moments, neutrinoless double beta decay, and pion decay measurements is discussed.
Fractures of the thoracolumbar spine in osteoporosis
Authors: Komadina Radko , Bloemers Frank W. , Jug Marko , Wendt Klaus W. , Nau Christoph , Pape Hans-Christoph 
Published: September 2024

AbstractDue to increasing life expectancy, the prevalence of fractures caused by osteoporosis is raising. These fractures significantly reduce the quality of life in the elderly population. They represent both a disease and an injury simultaneously. While they were once treated solely with conservative methods, new techniques and implants are expanding the indications for surgical treatment. This article presents the current treatment options.
Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests
Authors: Cheng Xiaoyan , Zhou Guohua , Chen Wei , Tan Lin , Long Qishi , Cui Fusheng , Tan Lei , Zou Guoxing , Tan Yong 
Published: September 2024

AbstractIn the past century, there have been great achievements in identifying resistance (R) genes and quantitative trait loci (QTLs) as well as revealing the corresponding molecular mechanisms for resistance in rice to major diseases and insect pests. The introgression of R genes to develop resistant rice cultivars has become the most effective and eco-friendly method to control pathogens/insects at present. However, little attention has been paid to durable and broad-spectrum resistance, which determines the real applicability of R genes. Here, we summarize all the R genes and QTLs conferring durable and broad-spectrum resistance in rice to fungal blast, bacterial leaf blight (BLB), and the brown planthopper (BPH) in molecular breeding. We discuss the molecular mechanisms and feasible methods of improving durable and broad-spectrum resistance to blast, BLB, and BPH. We will particularly focus on pyramiding multiple R genes or QTLs as the most useful method to improve durability and broaden the disease/insect spectrum in practical breeding regardless of its uncertainty. We believe that this review provides useful information for scientists and breeders in rice breeding for multiple stress resistance in the future.
Imaging the development of the human craniofacial arterial system – an experimental study
Authors: Jacobs K. , Langenbach G. E. J. , Docter D. , Cordewener P. A. M. , van de Beek B. J. , Korfage J. A. M. , Visser S. C. , Peters J. J. , Hagoort J. , Lobbezoo F. , de Bakker B. S. 
Published: September 2024

Abstract
Background
The process of vascular development is essential for shaping complex craniofacial structures. Investigating the interplay between vascular development and orofacial morphogenesis holds critical importance in clinical practice and contributes to advancing our comprehension of (vascular) developmental biology. New insights into specific vascular developmental pathways will have far-reaching implications across various medical disciplines, enhancing clinical understanding, refining surgical techniques, and elucidating the origins of congenital abnormalities. Embryonic development of the craniofacial vasculature remains, however, under-exposed in the current literature. We imaged and created 3-dimensional (D) reconstructed images of the craniofacial arterial system from two early-stage human embryonic samples.

Objective
The aim of this study was to investigate the vascular development of the craniofacial region in early-stage human embryos, with a focus on understanding the interplay between vascular development and orofacial morphogenesis.

Materials and methods
Reconstructions (3-D) were generated from high-resolution diffusible iodine-based contrast-enhanced computed tomography (diceCT) images, enabling visualization of the orofacial arterial system in human embryonic samples of Carnegie stages (CS) 14 and 18 from the Dutch Fetal Biobank, corresponding to weeks 7 and 8.5 of gestation.

Results
From two human embryonic samples (ages CS 14 and 18), the vascular development of the orofacial region at two different stages of development was successfully stained with B-Lugol and imaged using a micro-computed tomography (micro-CT) scanner with resolutions of 2.5-μm and 9-μm voxel sizes, respectively. Additionally, educational 3-D reconstructions of the orofacial vascular system were generated using AMIRA 2021.2 software.

Conclusion
Micro-CT imaging is an effective strategy for high-resolution visualization of vascular development of the orofacial region in human embryonic samples. The generated interactive 3-D educational models facilitate better understanding of the development of orofacial structures.

Graphical abstract
Maximum likelihood estimation for left-truncated log-logistic distributions with a given truncation point
Authors: Kreer Markus , Kızılersü Ayşe , Guscott Jake , Schmitz Lukas Christopher , Thomas Anthony W. 
Published: September 2024

AbstractFor a sample $$X_1, X_2,\ldots X_N$$

X
1

,

X
2

,
…

X
N

of independent identically distributed copies of a log-logistically distributed random variable X the maximum likelihood estimation is analysed in detail if a left-truncation point $$x_L>0$$

x
L

>
0

is introduced. Due to scaling properties it is sufficient to investigate the case $$x_L=1$$

x
L

=
1

. Here the corresponding maximum likelihood equations for a normalised sample (i.e. a sample divided by $$x_L$$

x
L

) do not always possess a solution. A simple criterion guarantees the existence of a solution: Let $$\mathbb {E}(\cdot )$$

E
(
·
)

denote the expectation induced by the normalised sample and denote by $$\beta _0=\mathbb {E}(\ln {X})^{-1}$$

β
0

=
E

(
ln
X
)

-
1

, the inverse value of expectation of the logarithm of the sampled random variable X (which is greater than $$x_L=1$$

x
L

=
1

). If this value $$\beta _0$$

β
0

is bigger than a certain positive number $$\beta _C$$

β
C

then a solution of the maximum likelihood equation exists. Here the number $$\beta _C$$

β
C

is the unique solution of a moment equation,$$\mathbb {E}(X^{-\beta _C})=\frac{1}{2}$$

E

(

X

-

β
C

)

=

1
2

. In the case of existence a profile likelihood function can be constructed and the optimisation problem is reduced to one dimension leading to a robust numerical algorithm. When the maximum likelihood equations do not admit a solution for certain data samples, it is shown that the Pareto distribution is the $$L^1$$

L
1

-limit of the degenerated left-truncated log-logistic distribution, where $$L^1(\mathbb {R}^+)$$

L
1

(

R

+

)

is the usual Banach space of functions whose absolute value is Lebesgue-integrable. A large sample analysis showing consistency and asymptotic normality complements our analysis. Finally, two applications to real world data are presented.
Elevated systemic venous pressures as a possible pathology in prepubertal pediatric idiopathic intracranial hypertension
Authors: Riedel Casper Schwartz , Norager Nicolas Hernandez , Bertelsen Maria , Mikkelsen Ronni , Juhler Marianne , Hansen Torben Skovbo 
Published: September 2024

Abstract
Background
Pediatric idiopathic intracranial hypertension (IIH) is a rare and challenging condition. As implied by the nomenclature, the etiologies remain unknown, and multiple etiologies are being investigated. In this study, we explored the potential role of increased systemic or cerebral venous pressure in the pathogenesis.

Method
An observational cohort study following the STROBE guidelines, including prepubertal children with clinical symptoms and imaging findings consistent with IIH referred to the neurosurgical department, was conducted. The patients underwent a comprehensive diagnostic protocol, including MRI, continuous intracranial pressure (ICP) monitoring, and endovascular venography with venous pressure measurements.

Results
The study included 11 consecutive patients (six boys and five girls) with an average age of 2.3 years, and an average BMI of 18.4. Among these, one patient was found to have venous stenosis with a gradient; the other 10 patients presented with normal intracranial anatomy. All patients exhibited elevated venous pressures, with an average superior sagittal sinus pressure of 18.9 mmHg, average internal jugular vein pressure of 17.0 mmHg, and average central venous pressure of 15.9 mmHg. Daytime ICP averaged 12.9 mmHg, whereas nighttime ICP averaged 17.2 mmHg with either A- or B-waves in 10 of the 11 patients. Despite pathological ICP, only three patients had papilledema.

Conclusions
All patients had an increased systemic venous pressure, indicating a possible pathological factor for prepubertal IIH. Additionally, our findings show that young children often only partly meet the Friedman criteria due to a lack of papilledema, emphasizing the need for pediatric-specific diagnostic criteria. Further large-scale studies are needed to confirm these findings and to explore the underlying reasons for this increase in venous pressure and potential new treatment avenues.