Miracle-dz/UniFAR-FTUs huggingface dataset:
Revealer: Detecting and Exploiting Regular Expression Denial-of-Service Vulnerabilities

Regular expression Denial-of-Service (ReDoS) is a class of algorithmic complexity attacks. Attackers can craft particular strings to trigger the worst-case super-linear matching time of some vulnerable regular expressions (regex) with extended features that are commonly supported by popular programming languages. ReDoS attacks can severely degrade the performance of web applications, which extensively employ regexes in their server-side logic. Nevertheless, the characteristics of vulnerable regexes with extended features remain understudied, making it difficult to mitigate or even detect such vulnerabilities.In this paper, we aim to model vulnerable regex patterns generated by popular regex engines and craft attack strings accordingly. Our characterization fully supports the analysis of regexes with any extended feature. We develop Revealer to detect vulnerable structures presented in any given regex and generate attack strings to exploit the corresponding vulnerabilities. Revealer takes a hybrid approach. It first statically locates potential vulnerable structures of a regex, then dynamically verifies whether the vulnerabilities can be triggered or not, and finally crafts attack strings that can lead to recursive backtracking. By combining both static analysis and dynamic analysis, Revealer can accurately and efficiently generate exploits in a limited amount of time. It can further offer mitigation suggestions based on the structural information it identifies.We implemented a prototype of Revealer for Java. We evaluated Revealer over a dataset with 29,088 regexes, and compared it with three state-of-the-art tools. The evaluation shows that Revealer considerably outperformed all the existing tools—Revealer can detect all 237 vulnerabilities that can be detected by any other tool, find 213 new vulnerabilities, and beat the best tool by 140.64%. We further demonstrate that Revealer successfully detected 45 vulnerable regexes in popular real-world applications. Our evaluation demonstrates that Revealer is both effective and efficient in detecting and exploiting ReDoS vulnerabilities.
Nanofluidic behavior at the interface of sectionalized hydrophobic/hydrophilic patterns in nanochannel

ABSTRACT We report a novel method to fabricate sectionalized hydrophobic/hydrophilic nanochannel. Photolithography, dry/wet etching, aligned anodic bonding and selective modification were utilized to fabricate nanochannel with four-sided surface patterns. Nanofluidic behavior was investigated by pressure driven method to study the relationship between pressure and meniscus position. Experimental results showed that evident delay happened to the flow before entering hydrophobic domain, the accumulative pressure required to pass through the hydrophobic section is significantly larger than hydrophilic section. This behavior may be attributed to the influence caused by the underlying wettability variation, especially under large surface-to-volume ratio in nanochannel.
Identification of Potential Biomarkers for Psoriasis by DNA Methylation and Gene Expression Datasets

DNA methylation (DNAm) plays an important role in the pathogenesis of psoriasis through regulating mRNA expressions. This study aimed to identify hub genes regulated by DNAm as biomarkers of psoriasis. Psoriatic skin tissues gene expression and methylation datasets were downloaded from Gene Expression Omnibus (GEO) database. Subsequently, multiple computational approaches, including immune infiltration analysis, enrichment analysis, protein–protein interaction (PPI) network establishment, and machine learning algorithm analysis (lasso, random forest, and SVM-RFE), were performed to analyze the regulatory networks, to recognize hub genes, and to clarify the pathogenesis of psoriasis. Finally, the hypermethylated genes were used to immune cell infiltration analysis, which revealed that psoriasis skin tissues were mainly composed of activated dendritic cells, resting mast cells, T follicular helper cells (cTfh), etc. Differentially expressed-methylated genes (DEMGs) were identified and partitioned into four subgroups and the 97 significantly hypermethylated and downregulated (hyper-down) genes accounted for the highest proportion (47%). Hyper-down genes were mainly enriched in glucose homeostasis, AMP-activated protein kinase (AMPK) signaling pathway, lipid storage disease, partial lipodystrophy, and insulin resistance. Furthermore, insulin receptor substrate 1 (IRS1), Rho guanine nucleotide exchange factor 10 (ARHGEF10) and retinoic acid induced 14 (RAI14) were identified as potential targets. These findings provided new ideas for future studies of psoriasis on the occurrence and the molecular mechanisms.
Molecular Properties and Therapeutic Targeting of the EBV-Encoded Receptor BILF1

Simple Summary The Epstein–Barr virus (EBV) is a γ-herpesvirus residing in over 90% of adults worldwide. Besides causing a benign glandular fever (infectious mononucleosis), EBV is also associated with a wide range of different types of cancers. This review will present these malignancies, current therapies, and summarize the present knowledge on an EBV-encoded oncogenic protein called BILF1. As a member of class A G protein–coupled receptors that are intrinsically successful drug targets, BILF1 will be discussed for its potential as future target in EBV-associated diseases. Finally, ongoing development of novel EBV-specific therapeutics is briefly outlined. Abstract The γ-herpesvirus Epstein–Barr Virus (EBV) establishes lifelong infections in approximately 90% of adults worldwide. Up to 1,000,000 people yearly are estimated to suffer from health conditions attributed to the infection with this virus, such as nasopharyngeal and gastric carcinomas as well as several forms of B, T and NK cell lymphoma. To date, no EBV-specific therapeutic option has reached the market, greatly reducing the survival prognoses of affected patients. Similar to other herpesviruses, EBV encodes for a G protein–coupled receptor (GPCR), BILF1, affecting a multitude of cellular signaling pathways. BILF1 has been identified to promote immune evasion and tumorigenesis, effectively ensuring a life-long persistence of EBV in, and driving detrimental health conditions to its host. This review summarizes the epidemiology of EBV-associated malignancies, their current standard-of-care, EBV-specific therapeutics in development, GPCRs and their druggability, and most importantly consolidates the findings of over 15 years of research on BILF1 in the context of EBV-specific drug development. Taken together, BILF1 constitutes a promising target for the development of novel EBV-specific therapeutics.
Annealing and Treatment Effects on Se Diffusion in CdTe Photovoltaics

The interdiffusion of CdTe and CdSe at the window layer interface to form alloyed CdSexTe1−x (CST) layers has been shown to improve the efficiency of CdTe photovoltaic devices, and there is evidence from the literature that Se passivates defects in these devices, particularly at grain boundaries. This work investigates the importance of the Cl treatment by comparing untreated, air-annealed and Cl treated CST devices to determine whether the Cl treatment is required for CST devices. We show that the Cl treatment increases Se diffusion and is still necessary for efficient CST devices, although it is not clear whether the efficiency gains are due to the effects of greater Se diffusion or the usual benefits of the Cl treatment on CdTe photovoltaics.
Bio-Morphological Reaction of Human Periodontal Ligament Fibroblasts to Different Types of Dentinal Derivates: In Vitro Study

Understanding the biological and morphological reactions of human cells towards different dentinal derivate grafting materials is fundamental for choosing the type of dentin for specific clinical situations. This study aimed to evaluate human periodontal ligament fibroblasts (hPLF) cells exposed to different dentinal derivates particles. The study design included the in vitro evaluation of mineralized dentine (SG), deproteinized and demineralized dentine (DDP), and demineralized dentine (TT) as test materials and of deproteinized bovine bone (BIOS) as the positive control material. The materials were kept with the hPLF cell line, and the evaluations were made after 24 h, 72 h, and 7 days of in vitro culture. The evaluated outcomes were proliferation by using XTT assays, the morphological characteristics by light microscopy (LM) and by the use of scanning electron microscopy (SEM), and adhesion by using confocal microscopy (CLSM). Overall, the experimental materials induced a positive response of the hPLFs in terms of proliferation and adhesion. The XTT assay showed the TT, and the SG induced significant growth compared to the negative control at 7 days follow-up. The morphological data supported the XTT assay: the LM observations showed the presence of densely packed cells with a modified shape; the SEM observations allowed the assessment of how fibroblasts exposed to DDP and TT presented cytoplasmatic extensions; and SG and BIOS also presented the thickening of the cellular membrane. The CLMS observations showed the expression of the proliferative marker, as well as and the expression of cytoskeletal elements involved in the adhesion process. In particular, the vinculin and integrin signals were stronger at 72 h, while the actin signal remained constantly expressed in all the follow-up of the sample exposed to SG material. The integrin signal was stronger at 72 h, and the vinculin and actin signals were stronger at 7 days follow-up in the sample exposed to DDP material. The vinculin and integrin signals were stronger at 72 h follow-up in the sample exposed to TT material; vinculin and integrin signals appear stronger at 24 h follow-up in the sample exposed to BIOS material. These data confirmed how dentinal derivates present satisfying biocompatibility and high conductivity and inductivity properties fundamental in the regenerative processes. Furthermore, the knowledge of the effects of the dentin’s degree of mineralization on cellular behavior will help clinicians choose the type of dentine derivates material according to the required clinical situation.
Robustness Analysis of Exponential Stability of Neutral-Type Nonlinear Systems With Multi-Interference

With a view to the unfavorable impact of the inevitable exogenous interferences for the practical engineering and signal transmission, here we focus on the robustness of global exponential stability for nonlinear dynamical systems subject to piecewise constant arguments, neutral terms and stochastic disturbances (SNPNDS). A new troublesome problem is that the neutral terms appeared in the derivative part affected on the other two interference factors is not a simple accumulation, so the Lipchitz condition is adopted to establish the ternary transcendental equations. However, different from previous transcendental equations with single or double variables, solving the transcendental equations with three variables becomes a bottleneck again. Hence, the special independent parameters & interdependent variables method targeted for SNPNDS is adopted here: firstly, all relative independent parameters are fixed. Next, the upper bounds of these three interdependent variables are orderly derived by their coupling relationship. Therein, the optimal constraint conditions for piecewise constant arguments and neutral terms are deduced. Through the strategies mentioned above, a class of algebraic problems of estimating three upper bounds by solving transcendental equations with three variables is settled. Besides, the main method ensures that the relationship built among these interference factors is mutually restrictive and dynamic. Meanwhile, the optimized constraints make the linkage effect more comprehensive and valid. Furthermore, the established mechanism is practical enough to be generalized to more multivariable systems. Finally, the numerical simulation comparisons are given to illustrate the validity of the derived results.
Deep Sequence Models for Text Classification Tasks

The exponential growth of data generated on the Internet in the current information age is a driving force for the digital economy. Extraction of information is the major value in an accumulated big data. Big data dependency on statistical analysis and hand-engineered rules machine learning algorithms are overwhelmed with vast complexities inherent in human languages. Natural Language Processing (NLP) is equipping machines to understand these human diverse and complicated languages. Text Classification is an NLP task which automatically identifies patterns based on predefined or undefined labeled sets. Common text classification application includes information retrieval, modeling news topic, theme extraction, sentiment analysis, and spam detection. In texts, some sequences of words depend on the previous or next word sequences to make full meaning; this is a challenging dependency task that requires the machine to be able to store some previous important information to impact future meaning. Sequence models such as RNN, GRU, and LSTM is a breakthrough for tasks with long-range dependencies. As such, we applied these models to Binary and Multi-class classification. Results generated were excellent with most of the models performing within the range of 80% and 94%. However, this result is not exhaustive as we believe there is room for improvement if machines are to compete with humans.
Common Kinetic Mechanism of Abasic Site Recognition by Structurally Different Apurinic/Apyrimidinic Endonucleases

Apurinic/apyrimidinic (AP) endonucleases Nfo (Escherichia coli) and APE1 (human) represent two conserved structural families of enzymes that cleave AP-site–containing DNA in base excision repair. Nfo and APE1 have completely different structures of the DNA-binding site, catalytically active amino acid residues and catalytic metal ions. Nonetheless, both enzymes induce DNA bending, AP-site backbone eversion into the active-site pocket and extrusion of the nucleotide located opposite the damage. All these stages may depend on local stability of the DNA duplex near the lesion. Here, we analysed effects of natural nucleotides located opposite a lesion on catalytic-complex formation stages and DNA cleavage efficacy. Several model DNA substrates that contain an AP-site analogue [F-site, i.e., (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran] opposite G, A, T or C were used to monitor real-time conformational changes of the tested enzymes during interaction with DNA using changes in the enzymes’ intrinsic fluorescence intensity mainly caused by Trp fluorescence. The extrusion of the nucleotide located opposite F-site was recorded via fluorescence intensity changes of two base analogues. The catalytic rate constant slightly depended on the opposite-nucleotide nature. Thus, structurally different AP endonucleases Nfo and APE1 utilise a common strategy of damage recognition controlled by enzyme conformational transitions after initial DNA binding.
Identification of Binge Drinkers via Convolutional Neural Network and Support Vector Machine

Studies have described neural and psychosocial markers of binge drinking. Deep learning would address how well these markers distinguish binge and non-binge drinkers. We examined the data of 180 binge and 282 non-binge drinking young adults from the Human Connectome Project. We randomly selected 90% of the subjects as training sample to build convolutional neural network (CNN) and support vector machine (SVM) models, and evaluated their performance in the remaining 10%. Imaging data were processed with published routines. 2D-/3D-CNN of gray matter volumes (GMV) exhibited an area under the curve (AUC) of 0.802/0.812 and SVM of psychosocial measures, GMVs and cortical thickness each exhibited an AUC of 0.883, 0.746 and 0.589 in the classification of binge and non-binge drinkers. Among the psychosocial measures, rule breaking behavior score showed the greatest difference and contributed most significantly to the classification in SVM model. Among the GMVs, left cerebellum showed the greatest difference in GMV and contributed most significantly to the classification in SVM model. These findings show that, associated with subtle cerebral volumetric differences, young adult binge drinking is best predicted by psvchosocial measures.
Factors Influencing Physicians’ Continuous Blogging: A Survey

Background: Health information can be more easily transmitted and diffused through the Internet, but questionable online health information often misinforms patients. Physicians have a duty to inform patients how to achieve positive health outcomes. Many physicians often write blogs to provide patients with the right health information. However, most articles available on this subject only describe the blog phenomena without providing a theoretical background and an empirical analysis of doctors using blogs. Methods: This study based on social cognitive theory (SCT) explores the factors influencing physicians’ intention of continuously blogging. A total of 887 physician bloggers were invited to participate in an online survey and 128 valid responses were received. Results: The SCT was proven to be useful in explaining 36.8% of the variation in physicians’ continuous intention to blog. Conclusions: We provide references for platform developers with different strategies to motivate doctors to blog, and the implications and limitations of this study are discussed.
Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.
A general potentiodynamic approach for red phosphorus and sulfur nanodot incorporation on reduced graphene oxide sheets: metal-free and binder-free electrodes for supercapacitor and hydrogen evolution activities

A general potentiodynamic strategy, for the first time, was proposed to incorporate red phosphorus (P) and sulfur (S) nanodots on reduced graphene oxide sheets (rGO) on a carbon fabric support. Uniformly embedded nanodots on rGO sheets were visualized using transmission electron microscopy. The as-prepared metal-free and binder-free electrodes can serve for both supercapacitors and the hydrogen evolution reaction. In particular, P nanodot incorporated rGO demonstrates a high specific capacitance of 334.2 F g−1, of which 99.2% is retained after 10 000 repeated charge/discharge cycles. Furthermore, this material delivers a current density of 10 mA cm−2 at an overpotential of −0.44 V versus RHE for the hydrogen evolution reaction in acidic medium.
ZDHHC19 Is Dispensable for Spermatogenesis, but Is Essential for Sperm Functions in Mice

Spermatogenesis is a complicated process involving mitotically proliferating spermatogonial cells, meiotically dividing spermatocytes, and spermatid going through maturation into spermatozoa. The post-translational modifications of proteins play important roles in this biological process. S-palmitoylation is one type of protein modifications catalyzed by zinc finger Asp-His-His-Cys (ZDHHC)-family palmitoyl S-acyltransferases. There are 23 mammalian ZDHHCs that have been identified in mouse. Among them, Zdhhc19 is highly expressed in adult testis. However, the in vivo function of Zdhhc19 in mouse spermatogenesis and fertility remains unknown. In this study, we knocked out the Zdhhc19 gene by generating a 2609 bp deletion from exon 3 to exon 6 in mice. No differences were found in testis morphology and testis/body weight ratios upon Zdhhc19 deletion. Spermatogenesis was not disrupted in Zdhhc19 knockout mice, in which properly developed TRA98+ germ cells, SYCP3+ spermatocytes, and TNP1+ spermatids/spermatozoa were detected in seminiferous tubules. Nevertheless, Zdhhc19 knockout mice were male infertile. Zdhhc19 deficient spermatozoa exhibited multiple defects including abnormal morphology of sperm tails and heads, decreased motility, and disturbed acrosome reaction. All of these led to the inability of Zdhhc19 mutant sperm to fertilize oocytes in IVF assays. Taken together, our results support the fact that Zdhhc19 is a testis enriched gene dispensable for spermatogenesis, but is essential for sperm functions in mice.
Boundary Control of Nonlinear ODE/Wave PDE Systems With a Spatially Varying Propagation Speed

We consider the boundary control of a nonlinear ordinary differential equation (ODE) actuated through a wave equation whose propagation speed is spatially varying. The ODE state is driven by the uncontrolled boundary of the wave equation. We design a nonlinear backstepping compensator to enable global asymptotic stability of the closed-loop system. We deduce the controller design and the stability proof by introducing a two-step backstepping transformation. The first transformation recasts the original system into a coupled $2\times 2$ first-order hyperbolic system with spatially varying coefficients cascading into a nonlinear ODE. The second transformation is used in the design of a compensator for the resulting cascaded system. Our design offers a global stability result that is guaranteed assuming that the spatially varying propagation speed is continuously differentiable and positive. Moreover, for nonlinear systems, our result is the first contribution enabling actual compensation of actuator delays governed by a coupled first-order hyperbolic partial differential equation (PDE) induced by a wave PDE dynamics with a spatially varying propagation speed. The validity of the proposed controller is illustrated by the benchmark system controlled via a cable.