bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adsorption Behavior and Tribological Properties of Surface-Capped Silica Nano-Additives in Rapeseed Oil
Authors: Li Ting , Yang Yule , Zhang Huanhuan , Song Ningning , Zhang Yujuan , Zhang Shengmao 
Published: November 2023

Abstract
The influence of particle size and surface modifier structure on the adsorption behavior and tribological properties of surface-capped silica nano-additives in rapeseed oil was investigated. With four kinds of SiO2 nanoparticles, methyl-modified DNS-2 (particle size 14 nm) and DNS-3 (particle size 5 nm), vinyl-modified RNS-D (particle size 5 nm), and epoxy-modified RNS-E (particle size 5 nm) as the nano-additives of rapeseed oil, their adsorption behavior in rapeseed oil was studied with a quartz crystal microbalance (QCM-D), and their tribological properties were evaluated with a four-ball friction and wear tester. DNS-2 with a larger particle size can form a high-strength tribo-film on the rubbed surface through shear sintering, thereby reducing the wear scar diameter of the steel ball. DNS-3, RNS-D, and RNS-E with smaller particle sizes can form a viscoelastic adsorption layer on the rubbed steel surface, and their equilibrium adsorption mass thereon increases with the increase of the polarity of the modifiers, which corresponds to the increases in their friction-reducing and anti-wear abilities as well as extreme pressure properties therewith. Particularly, the equilibrium adsorption mass and adsorption rate of RNS-E surface-capped by an epoxy group with the largest polarity are 16 times and 34 times higher than those of DNS-3 surface-capped by methyl. This indicates that encapsulating silica nanoparticles with strongly polar organic species could help to enhance its adsorption on rubbed metal surfaces and improve its tribological properties in rapeseed oil.
Cell-type-specific need of Ddx3 and PACT for interferon induction by RNA viruses
Authors: Sharma Nikhil , Kessler Patricia , Sen Ganes C. 
Published: November 2023

ABSTRACT
Virus infection of mammalian cells causes induction of interferon (IFN) synthesis, which, in turn, inhibits virus replication through the actions of the proteins encoded by the IFN-stimulated genes (ISG). Although, in general, ISGs inhibit virus replication in all cell types, there are reports that a few ISGs may function in a cell-specific manner. To address this issue systemically, we used an ISG shRNA library to screen two mouse cell lines, AML-12 and LA-4, for cell-specific actions of ISGs; Ddx3, an RNA helicase, was identified as such an ISG. It was required for both IFN action and IFN induction by the RIG-like receptor (RLR) pathway in AML-12 cells but not LA4 cells. In AML-12 cells, Ddx3 was required for the efficient translation of STAT1 and PACT mRNAs; ectopic expression of STAT1 and PACT in Ddx3-deficient cells restored IFN action and IFN induction, respectively. PACT was required for the activation of RLR signaling in AML-12 cells infected with vesicular stomatitis virus, Sendai virus (SeV), encephalomyocarditis virus (EMCV), or mouse hepatitis virus. Moreover, like PKR activation, RLR activation by PACT required S246 and S287 in its domain 3. This study demonstrated not only cell-specific action of an ISG, Ddx3, but also cell-specific need of PACT to trigger RLR signaling in RNA virus-infected cells.

IMPORTANCE
Interferon-stimulated genes (ISGs) are induced in response to interferon expression due to viral infections. Role of these ISGs can be variable in different cells or organs. Our study highlights such cell-specific role of an ISG, Ddx3, which regulates the translation of mRNAs essential for interferon induction (PACT) and interferon signaling (STAT1) in a cell-specific manner. Our study also highlights the role of PACT in RNA virus-induced RLR signaling. Our study depicts how Ddx3 regulates innate immune signaling pathways in an indirect manner. Such cell-specific behavior of ISGs helps us to better understand viral pathogenesis and highlights the complexities of viral tropism and innate immune responses.
Characterization of the genomes of cluster CT
Gordonia terrae
phages, Horseradish and Yummy
Authors: Bazinet Nicole , Biro Esther , Geydoshek Ashley , Hodgkin Grace , Jestel Eric , Klute Emily , MacDonald Clare , Russano Marcus , Thatcher Jayson , Neely Melody N. , Molloy Sally 
Published: November 2023

ABSTRACT

The genomes of lytic, cluster CT
Gordonia terrae
phages, Horseradish and Yummy, are 45,764 and 45,878 bp in length, respectively, and each encodes 71 protein-coding genes. The genomes are identical in sequence with the exception of a 38-bp insertion/deletion in the minor tail protein, gp26.
Genomic and transcriptomic analysis of
Ligilactobacillus salivarius
IBB3154—in search of new promoters for vaccine construction
Authors: Kobierecka Patrycja , Wyszyńska Agnieszka , Aleksandrzak-Piekarczyk Tamara , Sałańska Agnieszka , Gawor Jan , Bardowski Jacek , Jagusztyn Krynicka Katarzyna Elżbieta 
Published: November 2023

ABSTRACT

Transcriptomic analysis of the genome sequenced
Ligilactobacillus salivarius
strain IBB3154 grown at two different temperatures (37°C vs 42°C) identified differentially expressed genes involved in metabolic pathways, osmoregulation, and surface protein expression. Two highly expressed genes,
sasA1
and
sasA2
, which encode cell wall-anchored proteins belonging to the serine-rich repeat protein group, were found to be temperature-inducible. Moonlighting proteins with various functions, such as glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase, elongation factor Tu, and enolase, were highly expressed at both temperatures. The efficiency of promoters has been confirmed by the β-glucuronidase activity test; however, temperature dependence was not detected. We also found that the P

sasA1

promoter retained its activity in the presence of bile salts. Knowledge of promoters that are highly active in
L. salivarius
cells can be used to produce strains that are carriers of immunogenic proteins.

IMPORTANCE

The genome of the strain
Ligilactobacillus salivarius
IBB3154 was sequenced, and transcriptome analysis was carried out at two different temperatures, allowing the determination of gene expression levels in response to environmental changes (temperature). Genes with higher expression at 42°C were identified. The use of a reporter gene (β- glucuronidase) did not confirm the transcriptomic results; it was found that the promoters of the genes
sasA1
and
sasA2
were active in the presence of bile salts. This opens up new opportunities for the overexpression of genes of other bacterial species in
Ligilactobacillus
cells in the intestinal environment.
Optimizing environmental viral surveillance: bovine serum albumin increases RT-qPCR sensitivity for high pathogenicity avian influenza H5Nx virus detection from dust samples
Authors: Bessière Pierre , Hayes Brandon , Filaire Fabien , Lèbre Laetitia , Vergne Timothée , Pinson Matthieu , Croville Guillaume , Guérin Jean-Luc 
Published: November 2023

ABSTRACT
The latest outbreaks of high pathogenicity avian influenza viruses (HPAIVs) were the most widespread ever seen in Europe, entailing considerable economic costs and raising public health concerns. Virological surveillance protocols involve reverse transcription quantitative polymerase chain reactions (RT-qPCR) from tracheal and cloacal swabs, which are laborious to perform on a large scale and require special skills. Environmental sampling, and especially dust collection, may represent a relevant alternative, as it is cheap, non-invasive for animals, simpler, and quicker to carry out. The main drawback of dust samples is that they may contain high amounts of organic substances that can inhibit RT-qPCR reactions. Bovine serum albumin (BSA) is a molecule known to facilitate DNA polymerization in the presence of numerous inhibitors, including those from feces, litter, or food. We tested its use on dust samples collected on 107 farms localized in areas affected by epizootics of clade 2.3.4.4b HPAIV H5N1. We used a latent class modeling approach to compare the performance of three detection protocols: (i) BSA addition to the RT-qPCR reaction mix, (ii) dilution of template RNA, and (iii) a control protocol. Our results indicate that BSA addition to the RT-qPCR reaction mix improved the sensitivity of the method, by neutralizing inhibitors’ effect. Indeed, for hemagglutinin (HA) or matrix (M) RNA detection, the sensitivity of the BSA protocol was the highest, followed by that of the control protocol, and that of the dilution protocol. Our results suggest that the use of BSA could be routinely implemented in HPAIV dust monitoring RT-qPCR protocols.

IMPORTANCE
With the circulation of high pathogenicity avian influenza viruses having intensified considerably in recent years, the European Union is considering the vaccination of farmed birds. A prerequisite for this vaccination is the implementation of drastic surveillance protocols. Environmental sampling is a relevant alternative to animal sampling. However, environmental samples often contain inhibitory compounds in large enough quantities to inhibit RT-qPCR reactions. As bovine serum albumin is a molecule used in many fields to overcome this inhibitory effect, we tested its use on dust samples from poultry farms in areas heavily affected by HPAIV epizootics. Our results show that its use significantly increases the sensitivity of the method.
The Lost World: Characterizing and Detecting Undiscovered Test Smells
Authors: Yang Yanming , Hu Xing , Xia Xin , Yang Xiaohu 
Published: November 2023

Test smell refers to poor programming and design practices in testing and widely spreads throughout software projects. Considering test smells have negative impacts on the comprehension and maintenance of test code and even make code-under-test more defect-prone, it thus has great importance in mining, detecting, and refactoring them. Since Deursen et al. introduced the definition of “test smell”, several studies worked on discovering new test smells from test specifications and software practitioners’ experience. Indeed, many bad testing practices are “observed” by software developers during creating test scripts rather than through academic research and are widely discussed in the software engineering community (e.g., Stack Overflow) [
70
,
94
]. However, no prior studies explored new bad testing practices from software practitioners’ discussions, formally defined them as new test smell types, and analyzed their characteristics, which plays a bad role for developers in knowing these bad practices and avoiding using them during test code development. Therefore, we pick up those challenges and act by working on systematic methods to explore new test smell types from one of the most mainstream developers’ Q&A platforms, i.e., Stack Overflow. We further investigate the harmfulness of new test smells and analyze possible solutions for eliminating them. We find that some test smells make it hard for developers to fix failed test cases and trace their failing reasons. To exacerbate matters, we have identified two types of test smells that pose a risk to the accuracy of test cases. Next, we develop a detector to detect test smells from software. The detector is composed of six detection methods for different smell types. These detection methods are both wrapped with a set of syntactic rules based on the code patterns extracted from different test smells and developers’ code styles. We manually construct a test smell dataset from seven popular Java projects and evaluate the effectiveness of our detector on it. The experimental results show that our detector achieves high performance in precision, recall, and F1 score. Then, we utilize our detector to detect smells from 919 real-world Java projects to explore whether the six test smells are prevalent in practice. We observe that these test smells are widely spread in 722 out of 919 Java projects, which demonstrates that they are prevalent in real-world projects. Finally, to validate the usefulness of test smells in practice, we submit 56 issue reports to 53 real-world projects with different smells. Our issue reports achieve 76.4% acceptance by conducting sentiment analysis on developers’ replies. These evaluations confirm the effectiveness of our detector and the prevalence and practicality of new test smell types on real-world projects.
Coherence Attacks and Countermeasures in Interposer-based Chiplet Systems
Authors: Chacon Gino A. , Williams Charles , Knechtel Johann , Sinanoglu Ozgur , Gratz Paul V. , Soteriou Vassos 
Published: November 2023

Industry is moving towards large-scale hardware systems that bundle processor cores, memories, accelerators, and so on. via 2.5D integration. These components are fabricated separately as chiplets and then integrated using an interposer as an interconnect carrier. This new design style is beneficial in terms of yield and economies of scale, as chiplets may come from various vendors and are relatively easy to integrate into one larger sophisticated system. However, the benefits of this approach come at the cost of new security challenges, especially when integrating chiplets that come from untrusted or not fully trusted, third- party vendors.
In this work, we explore these challenges for modern interposer-based systems of cache-coherent, multi-core chiplets. First, we present basic coherence-oriented hardware Trojan attacks that pose a significant threat to chiplet-based designs and demonstrate how these basic attacks can be orchestrated to pose a significant threat to interposer-based systems. Second, we propose a novel scheme using an active interposer as a generic, secure-by-construction platform that forms a physical root of trust for modern 2.5D systems. The implementation of our scheme is confined to the interposer, resulting in little cost and leaving the chiplets and coherence system untouched. We show that our scheme prevents a range of coherence attacks with low overheads on system performance, ∼4%. Further, we demonstrate that our scheme scales efficiently as system size and memory capacities increase, resulting in reduced performance overheads.
A PERK-Specific Inhibitor Blocks Metastatic Progression by Limiting Integrated Stress Response–Dependent Survival of Quiescent Cancer Cells
Authors: Calvo Veronica , Zheng Wei , Adam-Artigues Anna , Staschke Kirk A. , Huang Xin , Cheung Julie F. , Nobre Ana Rita , Fujisawa Sho , Liu David , Fumagalli Maria , Surguladze David , Stokes Michael E. , Nowacek Ari , Mulvihill Mark , Farias Eduardo F. , Aguirre-Ghiso Julio A. 
Published: November 2023

Abstract

Purpose:
The integrated stress response (ISR) kinase PERK serves as a survival factor for both proliferative and dormant cancer cells. We aim to validate PERK inhibition as a new strategy to specifically eliminate solitary disseminated cancer cells (DCC) in secondary sites that eventually reawake and originate metastasis.

Experimental Design:
A novel clinical-grade PERK inhibitor (HC4) was tested in mouse syngeneic and PDX models that present quiescent/dormant DCCs or growth-arrested cancer cells in micro-metastatic lesions that upregulate ISR.

Results:
HC4 significantly blocks metastasis, by killing quiescent/slow-cycling ISRhigh, but not proliferative ISRlow DCCs. HC4 blocked expansion of established micro-metastasis that contained ISRhigh slow-cycling cells. Single-cell gene expression profiling and imaging revealed that a significant proportion of solitary DCCs in lungs were indeed dormant and displayed an unresolved ER stress as revealed by high expression of a PERK-regulated signature. In human breast cancer metastasis biopsies, GADD34 expression (PERK-regulated gene) and quiescence were positively correlated. HC4 effectively eradicated dormant bone marrow DCCs, which usually persist after rounds of therapies. Importantly, treatment with CDK4/6 inhibitors (to force a quiescent state) followed by HC4 further reduced metastatic burden. In HNSCC and HER2+ cancers HC4 caused cell death in dormant DCCs. In HER2+ tumors, PERK inhibition caused killing by reducing HER2 activity because of sub-optimal HER2 trafficking and phosphorylation in response to EGF.

Conclusions:
Our data identify PERK as a unique vulnerability in quiescent or slow-cycling ISRhigh DCCs. The use of PERK inhibitors may allow targeting of pre-existing or therapy-induced growth arrested “persister” cells that escape anti-proliferative therapies.
Selective DNA-PK Inhibition Enhances Chemotherapy and Ionizing Radiation Activity in Soft-Tissue Sarcomas
Authors: Laroche-Clary Audrey , Josensi Coralie , Derieppe Marie-Alix , Belhomme Sarah , Vendrely Véronique , Perret Raul , Cadogan Elaine , Italiano Antoine 
Published: November 2023

Abstract

Purpose:
Patients with advanced soft-tissue sarcomas (STS) exhibit a poor prognosis and have few therapeutic options. DNA-dependent protein kinase (DNA-PK) catalytic subunit is a multifunctional serine–threonine protein kinase that plays a crucial role in DNA double-strand damage repair via nonhomologous end joining.

Experimental Design:
To investigate the therapeutic potential of DNA-PK targeting in STS, we first evaluated the prognostic value of DNA-PK expression in two large cohorts of patients with STS. We then used the potent and selective DNA-PK inhibitor AZD7648 compound to investigate the antitumor effect of the pharmacologic inhibition of DNA-PK in vitro via MTT, apoptosis, cell cycle, and proliferation assays. In vivo studies were performed with patient-derived xenograft models to evaluate the effects of AZD7648 in combination with chemotherapy or ionizing radiation on tumor growth. The mechanisms of sensitivity and resistance to DNA-PK inhibition were investigated by using a genome-wide CRISPR-Cas9 positive screen.

Results:
DNA-PK overexpression is significantly associated with poor prognosis in patients with sarcomas. Selective pharmacologic inhibition of DNA-PK strongly synergizes with radiation- and doxorubicin-based regimen in sarcoma models. By using a genome-wide CRISPR-Cas9 positive screen, we identified genes involved in sensitivity to DNA-PK inhibition.

Conclusions:
DNA-PK inhibition deserves clinical investigation to improve response to current therapies in patients with sarcoma.
Performance of Cardiovascular Risk Prediction Models in Korean Patients With New‐Onset Rheumatoid Arthritis: National Cohort Study
Authors: Kim Jae Hyun , Lee Gaeun , Hwang Jinseub , Kim Ji‐Won , Kwon Jin‐Won , Song Yun‐Kyoung 
Published: November 2023

Background
This study aimed to compare the performance of established cardiovascular risk algorithms in Korean patients with new‐onset rheumatoid arthritis.

Methods and Results
This retrospective cohort study identified patients newly diagnosed with rheumatoid arthritis without a history of cardiovascular diseases between 2013 and 2019 using the National Health Insurance Service database. The cohort was followed up until 2020 for the development of the first major adverse cardiovascular event. General cardiovascular risk prediction algorithms, such as the systematic coronary risk evaluation model, the Korean risk prediction model for atherosclerotic cardiovascular diseases, the American College of Cardiology/American Heart Association pooled equations, and the Framingham Risk Score, were used. The discrimination and calibration of cardiovascular risk prediction models were evaluated. Hazard ratios were estimated using Cox proportional hazards regression. A total of 611 patients among 24 889 patients experienced a major adverse cardiovascular event during follow‐up. The median 10‐year atherosclerotic cardiovascular diseases risk score was significantly higher in patients with major adverse cardiovascular events than those without. The C‐statistics of risk algorithms ranged between 0.72 and 0.74. Compared with the low‐risk group, the actual risk of developing major adverse cardiovascular events increased significantly in the intermediate‐ and high‐risk groups for all algorithms. However, the risk predictions calculated from all algorithms overestimated the observed cardiovascular risk in the middle to high deciles, and only the systematic coronary risk evaluation algorithm showed comparable observed and predicted event rates in the low‐intermediate deciles with the highest sensitivity.

Conclusions
The systematic coronary risk evaluation model algorithm and the general risk prediction models discriminated patients with rheumatoid arthritis appropriately. However, overestimation should be considered when applying the cardiovascular risk prediction model in Korean patients.
Validation of an Integrated Genetic‐Epigenetic Test for the Assessment of Coronary Heart Disease
Authors: Philibert Robert , Dogan Timur K. , Knight Stacey , Ahmad Ferhaan , Lau Stanley , Miles George , Knowlton Kirk U. , Dogan Meeshanthini V. 
Published: November 2023

Background
Coronary heart disease (CHD) is the leading cause of death in the world. Unfortunately, many of the key diagnostic tools for CHD are insensitive, invasive, and costly; require significant specialized infrastructure investments; and do not provide information to guide postdiagnosis therapy. In prior work using data from the Framingham Heart Study, we provided in silico evidence that integrated genetic–epigenetic tools may provide a new avenue for assessing CHD.

Methods and Results
In this communication, we use an improved machine learning approach and data from 2 additional cohorts, totaling 449 cases and 2067 controls, to develop a better model for ascertaining symptomatic CHD. Using the DNA from the 2 new cohorts, we translate and validate the in silico findings into an artificial intelligence–guided, clinically implementable method that uses input from 6 methylation‐sensitive digital polymerase chain reaction and 10 genotyping assays. Using this method, the overall average area under the curve, sensitivity, and specificity in the 3 test cohorts is 82%, 79%, and 76%, respectively. Analysis of targeted cytosine‐phospho‐guanine loci shows that they map to key risk pathways involved in atherosclerosis that suggest specific therapeutic approaches.

Conclusions
We conclude that this scalable integrated genetic–epigenetic approach is useful for the diagnosis of symptomatic CHD, performs favorably as compared with many existing methods, and may provide personalized insight to CHD therapy. Furthermore, given the dynamic nature of DNA methylation and the ease of methylation‐sensitive digital polymerase chain reaction methodologies, these findings may pave a pathway for precision epigenetic approaches for monitoring CHD treatment response.