bluuebunny/crossref_metadata_2025_split huggingface dataset:
New insights into pathogenesis of congenital pseudarthrosis of tibia in children using periosteum proteomics analysis
Authors: Liu Yaoxi , Qin Zhen Qi , Zheng Yu , Wu Jiangyan , Yang Ge , Tan Qian , Zhu Guanghui , Liu Kun , Mei Haibo 
Published: August 2022

RationaleThe exact etiology and pathogenesis of congenital pseudarthrosis of tibia (CPT) are not clear. Quantitative proteomics analysis plays a vital role in disease pathology research. Tandem mass tag (TMT)‐based proteomics techniques were employed to identify and analyze the differentially expressed proteins (DEP) in the tibia periosteum tissues of CPT patients.MethodsThe samples were divided into three groups: CPT with NF1 group, CPT without NF1 group (non‐NF1‐CPT), and control group (patients with open tibial fracture). A fold change ≥1.5 or ≤0.66 and P‐value <0.05 were used as the thresholds to screen DEPs. Subsequently, bioinformatics resources such as online tools DAVID and String were used to generate gene ontology (GO) annotation, KEGG pathways enrichment, and protein–protein interaction (PPI) network for these DEPs.ResultsThe results show that a total of 347 proteins were differentially expressed in NF1‐CPT groups, 212 of which were upregulated and 135 were downregulated. There were more DEPs in non‐NF1‐CPT groups; we identified 467 DEPs, including 281 upregulated and 186 downregulated. Among them, NF1‐CPT groups and non‐NF1‐CPT groups shared 231 DEPs, and the remaining 230 DEPs showed the same expression trend in the two disease groups, with 117 upregulated and 113 downregulated. In particular, 116 proteins were altered only in NF1‐CPT groups (94 were upregulated and 22 were downregulated), whereas 236 proteins were altered only in non‐NF1‐CPT groups (164 were upregulated and 72 were downregulated). Finally, compared with non‐NF1‐CPT groups, 47 proteins changed 1.5‐fold and P‐value < 0.05 in NF1‐CPT groups.ConclusionsTo sum up, we found that common DEPS in periosteum of NF1‐CPT and non‐NF1‐CPT groups are mainly involved in cell matrix assembly, cell adhesion, AKT‐PI3K signal pathway activation, and vascular agglutination, which indicate that these are the pathological characteristics of CPT. The osteogenic ability is weak, the osteoclastic ability is strong, the vascular lumen is narrow, the invasive growth and the proliferation of fibroblasts are enhanced in CPT patients.
Infrared pulsed fiber laser‐produced silver‐109 nanoparticles for laser desorption/ionization mass spectrometry of 3‐hydroxycarboxylic acids
Authors: Kołodziej Artur , Płaza‐Altamer Aneta , Nizioł Joanna , Ruman Tomasz 
Published: August 2022

Rationale3‐Hydroxycarboxylic acids are one of the major components of bacterial lipopolysaccharides (LPS), also known as endotoxins. Endotoxins pose a serious health risk and can seriously damage the internal organs of humans and animals. 3‐Hydroxycarboxylic acids can be used as environmental markers to determine endotoxin levels. At the time of preparation of this manuscript no studies on laser mass spectrometry (MS) and analysis with silver nanoparticles (NP) for 3‐hydroxycarboxylic acids have been published in literature.MethodsSix acids, 3‐hydroxyoctanoic (3‐OH‐C8:0), 3‐hydroxydecanoic (3‐OH‐C10:0), 3‐hydroxydodecanoic (3‐OH‐C12:0), 3‐hydroxytetradecanoic (3‐OH‐C14:0), 3‐hydroxyhexadecanoic (3‐OH‐C16:0), and 3‐hydroxyoctadecanoic (3‐OH‐C18:0) acids, were used as test compounds on the target containing silver‐109 NPs for quantification using matrix‐assisted laser desorption/ionization (MALDI)–type mass spectrometer. Methods were also tested on spiked human blood serum samples to quantify 3‐hydroxycarboxylic acids and verify the influence of the biological matrix on the measurement.ResultsAnalyzed acids were directly tested in 1 000 000‐fold concentration change conditions ranging from 1 mg/mL to 1 ng/mL. The semi‐automatic MSI (MS imaging) method allowed us to obtain two to five times lower limit of detection (LOD) and lower limit of quantitation (LLOQ) values than common LDI (Bruker Daltonics, Bremen, Germany) method for analyzed acids. For almost all results of 3‐hydroxycarboxylic acids, the trendline fit was better for the semi‐automatic MSI method than the manual LDI method.ConclusionFor the first time, the use of laser MS for the quantification of 3‐hydroxycarboxylic acids has been demonstrated, and it has been proven that it can be used in the quantitative analysis of such compounds over a wide range of concentrations. In addition, a comparison of two methods—manual LDI‐MS and semi‐automatic MSI—is presented.
A case of slowly progressive malignant pericardial mesothelioma suggesting the involvement of BAP1 loss
Authors: Fukasawa Naoto , Agemi Yoko , Shiba Aya , Aga Masaharu , Hamakawa Yusuke , Miyazaki Kazuhito , Taniguchi Yuri , Misumi Yuki , Shimokawa Tsuneo , Ono Kyoko , Hayashi Hiroyuki , Okamoto Hiroaki 
Published: August 2022

AbstractMalignant pericardial mesothelioma (MPM) is a rare tumour that arises from the mesothelial cells of the pericardium. No standard treatment has been established owing to a poor treatment response; therefore, MPM has a poor prognosis. We herein report a rare case of MPM in a 70‐year‐old man that was diagnosed immunohistopathologically using cell block sections of pericardial fluid and in which long‐term survival for more than 3 years was achieved with only periodic pericardial drainage. Immunohistopathological staining investigations, especially BRCA1‐associated protein 1 (BAP1) immunostaining using cell block sections of pericardial effusion, are effective in making a diagnosis of MPM. Well‐differentiated papillary mesothelioma (WDPM) with BAP1 loss progresses to MPM in the long term, showing that BAP1 loss may induce phenotypical evolution of WDPM. BAP1 loss may also progress to malignant mesothelioma in situ and then to invasive mesothelioma. BAP1 immunohistochemistry should be considered for the early diagnosis of MPM.
High Pressure Rapid Synthesis of LiCrTiO4 with Oxygen Vacancy for High Rate Lithium‐Ion Battery Anodes
Authors: Yan Lv , Qin Jieming , Liang Benkuan , Gao Shanlin , Wang Bo , Cui Jiuyue , Bolag Altan , Yang Yanchun 
Published: August 2022

AbstractLithium‐ion battery based on LiCrTiO4 (LCTO) is considered to be a promising anode material, as they provide higher safety and durability beyond than that of graphite electrode. However, the applications of this transformative technology demand improved inherent electrical conductivity of LCTO as well as a simple and rapid synthetic route. Here, LCTO with oxygen vacancies (OVs) is fabricated using high‐pressure synthesis technology in only 40 min. The optimal synthesis pressure is 0.8 GPa (LCTO‐0.8). The reversible capacity of LCTO‐0.8 at 1C is 131 mA h g−1 after 1000 cycles and the capacity retention is nearly 97%, and the reversible capacity of LCTO synthesized at atmospheric pressure (LCTO‐P) is 85 mA h g−1 under the same circumstances. Even at 5C, the reversible capacity is 110 mA h g−1, which is 77% higher than LCTO‐P. Furthermore, it is confirmed by theoretical calculations that the introduction of OVs has the occupation of electronic states at the Fermi level, which greatly enhances the intrinsic conductivity of LCTO. Specifically, the electronic conductivity has increased by two orders of magnitude compared with LCTO‐P. Therefore, high‐pressure synthesis technology endows LCTO with superior characteristics, providing a new avenue for industrialization.
Experimental methods for the analysis of the tensile behavior of concrete joints
Authors: Höffgen Jan P. , Mohs Matthias , Sonderegger Eric , Malárics‐Pfaff Viktória , Dehn Frank 
Published: August 2022

AbstractAdhesion plays an important role in the evaluation of hydraulic structures with unreinforced concrete joints. The experimental determination of joint tensile strength as a quantifiable parameter is not standardized, resulting in a variety of test setups found in literature. The present paper highlights advantages and disadvantages of three of the most common tension tests for plain concrete and concrete joints through both theoretical and laboratory experimental analysis on specimens with artificial joints. Splitting tension tests were found to be inexpensive but tend to overestimate the adhesive strength of weak joints. Direct tension tests require an elaborate test setup but may yield information on the tension softening behavior. Pull‐off tests stand out for their ability to yield in‐situ results but deliver inconclusive results.
Engineering gold nanoparticles for molecular diagnostics and biosensing
Authors: Oliveira Beatriz B. , Ferreira Daniela , Fernandes Alexandra R. , Baptista Pedro Viana 
Published: August 2022

AbstractAdvances in nanotechnology and medical science have spurred the development of engineered nanomaterials and nanoparticles with particular focus on their applications in biomedicine. In particular, gold nanoparticles (AuNPs) have been the focus of great interest, due to their exquisite intrinsic properties, such as ease of synthesis and surface functionalization, tunable size and shape, lack of acute toxicity and favorable optical, electronic, and physicochemical features, which possess great value for application in biodetection and diagnostics purposes, including molecular sensing, photoimaging, and application under the form of portable and simple biosensors (e.g., lateral flow immunoassays that have been extensively exploited during the current COVID‐19 pandemic). We shall discuss the main properties of AuNPs, their synthesis and conjugation to biorecognition moieties, and the current trends in sensing and detection in biomedicine and diagnostics.This article is categorized under:
Diagnostic Tools > Biosensing
Diagnostic Tools > In Vitro Nanoparticle‐Based Sensing
Diagnostic Tools > In Vivo Nanodiagnostics and Imaging
Neural Network Robustness as a Verification Property: A Principled Case Study
Authors: Casadio Marco , Komendantskaya Ekaterina , Daggitt Matthew L. , Kokke Wen , Katz Guy , Amir Guy , Refaeli Idan 
Published: August 2022

AbstractNeural networks are very successful at detecting patterns in noisy data, and have become the technology of choice in many fields. However, their usefulness is hampered by their susceptibility to adversarial attacks. Recently, many methods for measuring and improving a network’s robustness to adversarial perturbations have been proposed, and this growing body of research has given rise to numerous explicit or implicit notions of robustness. Connections between these notions are often subtle, and a systematic comparison between them is missing in the literature. In this paper we begin addressing this gap, by setting up general principles for the empirical analysis and evaluation of a network’s robustness as a mathematical property—during the network’s training phase, its verification, and after its deployment. We then apply these principles and conduct a case study that showcases the practical benefits of our general approach.
Affine Loop Invariant Generation via Matrix Algebra
Authors: Ji Yucheng , Fu Hongfei , Fang Bin , Chen Haibo 
Published: August 2022

AbstractLoop invariant generation, which automates the generation of assertions that always hold at the entry of a while loop, has many important applications in program analysis and formal verification. In this work, we target an important category of while loops, namely affine while loops, that are unnested while loops with affine loop guards and variable updates. Such a class of loops widely exists in many programs yet still lacks a general but efficient approach to invariant generation. We propose a novel matrix-algebra approach to automatically synthesizing affine inductive invariants in the form of an affine inequality. The main novelty of our approach is that (i) the approach is general in the sense that it theoretically addresses all the cases of affine invariant generation over an affine while loop, and (ii) it can be efficiently automated through matrix-algebra (such as eigenvalue, matrix inverse) methods.The details of our approach are as follows. First, for the case where the loop guard is a tautology (i.e., ‘true’), we show that the eigenvalues and their eigenvectors of the matrices derived from the variable updates of the loop body encompass all meaningful affine inductive invariants. Second, for the more general case where the loop guard is a conjunction of affine inequalities, our approach completely addresses the invariant-generation problem by first establishing through matrix inverse the relationship between the invariants and a key parameter in the application of Farkas’ lemma, then solving the feasible domain of the key parameter from the inductive conditions, and finally illustrating that a finite number of values suffices for the key parameter w.r.t a tightness condition for the invariants to be generated.Experimental results show that compared with previous approaches, our approach generates much more accurate affine inductive invariants over affine while loops from existing and new benchmarks within a few seconds, demonstrating the generality and efficiency of our approach.
Data-driven Numerical Invariant Synthesis with Automatic Generation of Attributes
Authors: Bouajjani Ahmed , Boutglay Wael-Amine , Habermehl Peter 
Published: August 2022

AbstractWe propose a data-driven algorithm for numerical invariant synthesis and verification. The algorithm is based on the ICE-DT schema for learning decision trees from samples of positive and negative states and implications corresponding to program transitions. The main issue we address is the discovery of relevant attributes to be used in the learning process of numerical invariants. We define a method for solving this problem guided by the data sample. It is based on the construction of a separator that covers positive states and excludes negative ones, consistent with the implications. The separator is constructed using an abstract domain representation of convex sets. The generalization mechanism of the decision tree learning from the constraints of the separator allows the inference of general invariants, accurate enough for proving the targeted property. We implemented our algorithm and showed its efficiency.
Abstraction Modulo Stability for Reverse Engineering
Authors: Becchi Anna , Cimatti Alessandro 
Published: August 2022

AbstractThe analysis of legacy systems requires the automated extraction of high-level specifications. We propose a framework, called Abstraction Modulo Stability, for the analysis of transition systems operating in stable states, and responding with run-to-completion transactions to external stimuli. The abstraction captures the effects of external stimuli on the system state, and describes it in the form of a finite state machine. This approach is parametric on a set of predicates of interest and the definition of stability. We consider some possible stability definitions which yield different practically relevant abstractions, and propose a parametric algorithm for abstraction computation. The obtained FSM is extended with guards and effects on a given set of variables of interest. The framework is evaluated in terms of expressivity and adequacy within an industrial project with the Italian Railway Network, on reverse engineering tasks of relay-based interlocking circuits to extract specifications for a computer-based reimplementation.
Reachability of Koopman Linearized Systems Using Random Fourier Feature Observables and Polynomial Zonotope Refinement
Authors: Bak Stanley , Bogomolov Sergiy , Hencey Brandon , Kochdumper Niklas , Lew Ethan , Potomkin Kostiantyn 
Published: August 2022

AbstractKoopman operator linearization approximates nonlinear systems of differential equations with higher-dimensional linear systems. For formal verification using reachability analysis, this is an attractive conversion, as highly scalable methods exist to compute reachable sets for linear systems. However, two main challenges are present with this approach, both of which are addressed in this work. First, the approximation must be sufficiently accurate for the result to be meaningful, which is controlled by the choice ofobservable functionsduring Koopman operator linearization. By using random Fourier features as observable functions, the process becomes more systematic than earlier work, while providing a higher-accuracy approximation. Second, although the higher-dimensional system is linear, simple convex initial sets in the original space can become complex non-convex initial sets in the linear system. We overcome this using a combination of Taylor model arithmetic and polynomial zonotope refinement. Compared with prior work, the result is more efficient, more systematic and more accurate.
STLmc: Robust STL Model Checking of Hybrid Systems Using SMT
Authors: Yu Geunyeol , Lee Jia , Bae Kyungmin 
Published: August 2022

AbstractWe present theSTLmcmodel checker for signal temporal logic (STL) properties of hybrid systems. TheSTLmctool can perform STL model checking up to a robustness threshold for a wide range of hybrid systems. Our tool utilizes the refutation-complete SMT-based bounded model checking algorithm by reducing the robust STL model checking problem into Boolean STL model checking. IfSTLmcdoes not find a counterexample, the system is guaranteed to be correct up to the given bounds and robustness threshold. We demonstrate the effectiveness ofSTLmcon a number of hybrid system benchmarks.
Shared Certificates for Neural Network Verification
Authors: Fischer Marc , Sprecher Christian , Dimitrov Dimitar Iliev , Singh Gagandeep , Vechev Martin 
Published: August 2022

AbstractExisting neural network verifiers compute a proof that each input is handled correctly under a given perturbation by propagating a symbolic abstraction of reachable values at each layer. This process is repeated from scratch independently for each input (e.g., image) and perturbation (e.g., rotation), leading to an expensive overall proof effort when handling an entire dataset. In this work, we introduce a new method for reducing this verification cost without losing precision based on a key insight that abstractions obtained at intermediate layers for different inputs and perturbations can overlap or contain each other. Leveraging our insight, we introduce the general concept of shared certificates, enabling proof effort reuse across multiple inputs to reduce overall verification costs. We perform an extensive experimental evaluation to demonstrate the effectiveness of shared certificates in reducing the verification cost on a range of datasets and attack specifications on image classifiers including the popular patch and geometric perturbations. We release our implementation at https://github.com/eth-sri/proof-sharing.
Methode zur abstrakten Modellierung von Automotive Systems-on-Chips
Authors: Kirchner Aljoscha 
Published: August 2022

ZusammenfassungIm folgenden Kapitel wird das Konzept der in dieser Arbeit entwickelten Entwicklungsmethode zur abstrakten Modellierung von Automotive Systems-on-Chips vorgestellt. Teile der Methode sowie eine Zusammenfassung der Entwicklungsmethode wurden bereits in den Arbeiten [76], [77], [78] und [79] veröffentlicht. Das übergeordnete Ziel der Methode ist hierbei die Steigerung der Effizienz über alle Phasen der SoC-Entwicklung hinweg.
Zusammenfassung und Ausblick
Authors: Kirchner Aljoscha 
Published: August 2022

ZusammenfassungIm folgenden Kapitel wird die hier vorliegende Arbeit zusammengefasst. Dazu wird auf die in dieser Arbeit vorgestellte modellbasierte Entwicklungsmethode eingegangen. Zudem werden die daraus resultierenden Ergebnisse in gekürzter Form dargestellt.
M5-branes wrapped on four-dimensional orbifolds
Authors: Cheung K. C. Matthew , Fry Jacob H. T. , Gauntlett Jerome P. , Sparks James 
Published: August 2022

Abstract
We construct supersymmetric AdS3 solutions of D = 11 supergravity, dual to d = 2, $$ \mathcal{N} $$
N
= (0, 2) SCFTs, that are associated with M5-branes wrapping two different four-dimensional orbifolds. In one case the orbifold is a spindle fibred over another spindle, while in the other it is a spindle fibred over a Riemann surface with genus g > 1. We show that the central charges of the d = 2 SCFTs calculated from the gravity solutions agree with field theory computations using anomaly polynomials. The new D = 11 solutions are obtained after constructing a new consistent Kaluza-Klein truncation of maximal D = 7 gauged supergravity reduced on a spindle down to D = 5 minimal gauged supergravity.
Genetic basis of sorghum leaf width and its potential as a surrogate for transpiration efficiency
Authors: Zhi Xiaoyu , Hammer Graeme , Borrell Andrew , Tao Yongfu , Wu Alex , Hunt Colleen , van Oosterom Erik , Massey-Reed Sean Reynolds , Cruickshank Alan , Potgieter Andries B. , Jordan David , Mace Emma , George-Jaeggli Barbara 
Published: August 2022

Abstract
Key message
Leaf width was correlated with plant-level transpiration efficiency and associated with 19 QTL in sorghum, suggesting it could be a surrogate for transpiration efficiency in large breeding program.

Abstract
Enhancing plant transpiration efficiency (TE) by reducing transpiration without compromising photosynthesis and yield is a desirable selection target in crop improvement programs. While narrow individual leaf width has been correlated with greater intrinsic water use efficiency in C4 species, the extent to which this translates to greater plant TE has not been investigated. The aims of this study were to evaluate the correlation of leaf width with TE at the whole-plant scale and investigate the genetic control of leaf width in sorghum. Two lysimetry experiments using 16 genotypes varying for stomatal conductance and three field trials using a large sorghum diversity panel (n = 701 lines) were conducted. Negative associations of leaf width with plant TE were found in the lysimetry experiments, suggesting narrow leaves may result in reduced plant transpiration without trade-offs in biomass accumulation. A wide range in width of the largest leaf was found in the sorghum diversity panel with consistent ranking among sorghum races, suggesting that environmental adaptation may have a role in modifying leaf width. Nineteen QTL were identified by genome-wide association studies on leaf width adjusted for flowering time. The QTL identified showed high levels of correspondence with those in maize and rice, suggesting similarities in the genetic control of leaf width across cereals. Three a priori candidate genes for leaf width, previously found to regulate dorsoventrality, were identified based on a 1-cM threshold. This study provides useful physiological and genetic insights for potential manipulation of leaf width to improve plant adaptation to diverse environments.
Risk Assessment and Hazardous Effects of Metal Contamination in O. niloticus and S. galilaeus from Four Islands of the River Nile
Authors: Elhaddad Engy , Salaah Sally M. , Salama Hanan M. M. , El-Sherif Dina M. , Gaber Hanan S. 
Published: August 2022

AbstractThe Nile River islands are recognized as the most productive lands in Egypt. Although, these islands are vulnerable to several natural and man-made crises. The present study was aimed to evaluate the consequences of different anthropogenic activities on the heavy metals load and histological alterations inO. niloticusandS. galilaeuscollected from four different Nile River islands along the Great Cairo sector (Egypt), and the possible health risks for human consumers. Metals were accumulated in both fish muscles in the following order: Fe > Zn > Cu > Mn > Pb.S. galilaeuswas recorded higher metal pollution index thanO. niloticus, while El-Warrak Island was documented the highest MPI and hazard quotient among all sampling sites. All sampled tissues were recorded histopathological lesions in both fish. The present study may be considered as an early alert for habitual consumers, particularly at high consumption rates of some fish species.