bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum thymidine kinase 1 protein concentrations and presence of its autoantibody as biomarkers for screening dogs with malignant tumors
Authors: Kim Yoonhee , Park Jeongjoo , Kim Byunggak , Yu Kyung‐Rok , Kim Hong Sook , Oh Yein , Seo Kyoungwon , Ryu Minok , Park Chul , Bhang Dongha , Choi Ulsoo , Youn Hwayoung 
Published: December 2023

AbstractBackgroundAn accurate and easily accessible method for diagnosing malignancies in local veterinary clinics has not yet been established.ObjectivesTo investigate the usefulness of serum thymidine kinase 1 (TK1) protein and its autoantibody as tumor biomarkers in dogs.AnimalsSerum samples from 1702 dogs were collected from local animal hospitals and referral animal medical centers in South Korea.MethodsTK1 protein OD value and TK1 autoantibody ratio (TK1 autoantibody OD/total IgG OD) in serum samples of dogs classified into healthy controls, group with nontumor disease, group with benign and group with malignant tumors were measured using lateral flow immunochromatographic assay methods.ResultsTK1 autoantibody levels were significantly higher in malignant tumor group (median 0.71) than in healthy controls (median 0.34), group with nontumor disease (median 0.34), and group with benign tumor (median 0.32, Welch t test, P < .0001). They were also significantly different among dogs with carcinomas (median 0.77), hematopoietic tumors (median 0.71), and sarcomas (median 0.56) than in healthy controls (median 0.34, post hoc Games‐Howell test, P < .0001). In the receiver operating characteristic curve of TK1 protein, AUC was 0.633 (95% CI: 0.592‐0.675, P < .0001). The AUC of TK1 autoantibody ratio was 0.758 (95% CI: 0.723‐0.793, P < .0001).Conclusions and Clinical ImportanceTK1 autoantibody is a potentially useful biomarker for differentiating between healthy and tumor‐bearing dogs, better than TK1 protein measurement. However, both were inadequate when used as single biomarkers for screening dogs to discover occult malignant tumors.
Root‐exuded benzoxazinoids can alleviate negative plant–soil feedbacks
Authors: Gfeller Valentin , Thoenen Lisa , Erb Matthias 
Published: December 2023

Summary

Plants can suppress the growth of other plants by modifying soil properties. These negative plant–soil feedbacks are often species‐specific, suggesting that some plants possess resistance strategies. However, the underlying mechanisms remain largely unknown.

Here, we investigated whether benzoxazinoids, a class of dominant secondary metabolites that are exuded into the soil by maize and other cereals, allow maize plants to cope with plant–soil feedbacks.

We find that three out of five tested crop species reduce maize (Zea mays L.) performance via negative plant–soil feedbacks relative to the mean across species. This effect is partially alleviated by the capacity of maize plants to produce benzoxazinoids. Soil complementation with purified benzoxazinoids restores the protective effect for benzoxazinoid‐deficient mutants. Sterilization and reinoculation experiments suggest that benzoxazinoid‐mediated protection acts via changes in soil biota. Substantial variation of the protective effect between experiments and soil types illustrates context dependency.

In conclusion, exuded plant secondary metabolites allow plants to cope with plant–soil feedbacks. These findings expand the functional repertoire of plant secondary metabolites and reveal a mechanism by which plants can resist negative effects of soil feedbacks. The uncovered phenomenon may represent a promising avenue to stabilize plant performance in crop rotations.
Exploration in the Mechanism of Ginsenoside Rg5 for the Treatment of Osteosarcoma by Network Pharmacology and Molecular Docking
Authors: Liu Ming‐yang , Jiang Dong‐xin , Zhao Xiang , Zhang Liang , Zhang Yu , Liu Zhen‐dong , Liu Run‐ze , Li Hai‐jun , Rong Xiao‐yu , Gao Yan‐zheng 
Published: December 2023

ObjectiveOsteosarcoma is a primary malignancy originating from mesenchymal tissue characterized by rapid growth, early metastasis and poor prognosis. Ginsenoside Rg5 (G‐Rg5) is a minor ginsenoside extracted from Panax ginseng C.A. Meyer which has been discovered to possess anti‐tumor properties. The objective of current study was to explore the mechanism of G‐Rg5 in the treatment of osteosarcoma by network pharmacology and molecular docking technology.MethodsPharmmapper, SwissTargetPrediction and similarity ensemble approach databases were used to obtain the pharmacological targets of G‐Rg5. Related genes of osteosarcoma were searched for in the GeneCards, OMIM and DrugBank databases. The targets of G‐Rg5 and the related genes of osteosarcoma were intersected to obtain the potential target genes of G‐Rg5 in the treatment of osteosarccoma. The STRING database and Cytoscape 3.8.2 software were used to construct the protein–protein interaction (PPI) network, and the Database for Annotation, Visualization and Integrated Discovery (DAVID) platform was used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. AutoDock vina software was used to perform molecular docking between G‐Rg5 and hub targets. The hub genes were imported into the Kaplan–Meier Plotter online database for survival analysis.ResultsA total of 61 overlapping targets were obtained. The related signaling pathways mainly included PI3K‐Akt signaling pathway, Proteoglycans in cancer, Lipid and atherosclerosis and Kaposi sarcoma‐associated herpesvirus infection. Six hub targets including PIK3CA, SRC, TP53, MAPK1, EGFR, and VEGFA were obtained through PPI network and targets‐pathways network analyses. The results of molecular docking showed that the binding energies were all less than –7 kcal/mol. And the results of survival analysis showed TP53 and VEGFA affect the prognosis of sarcoma patients.ConclusionThis study explored the possible mechanism of G‐Rg5 in the treatment of osteosarcoma using network pharmacology method, suggesting that G‐Rg5 has the characteristics of multi‐targets and multi‐pathways in the treatment of osteosarcoma, which lays a foundation for the follow‐up experimental and clinical researches on the therapeutic effects of G‐Rg5 on osteosarcoma.
Arteriovenous malformation with hair collar sign
Authors: Hollman Dylan , Alzahrani Fatmah , Fiorillo Loretta , Thompson Adrienne , Mahmood Muhammad N. 
Published: December 2023

AbstractWe report the case of a newborn who was noted at birth to have an occipital scalp nodule presenting with a hair collar sign (HCS). The nodule had enlarged since birth. An MRI revealed a soft tissue mass on the occipital scalp without deep extension or cranial bone involvement. A biopsy of the nodule led to a diagnosis of arteriovenous malformation (AVM). A vascular malformation with HCS has not been reported before in North America. This case highlights the complexity of diagnosing a lesion with a hair collar sign.
Multifaceted support for quality of life in childhood cancer survivors: Questionnaire survey
Authors: Hirano Naoki , Suenobu Souichi , Ihara Kenji 
Published: December 2023

AbstractBackgroundAlong with improvements in curative treatment for childhood cancer, childhood cancer survivors (CCSs) often face numerous problems such as late complications of cancer treatment, social issues at school, struggles in employment, and financial difficulties. These children have received a wide range of support from the medical, educational, and administrative sectors. However, it was unclear how this multifaceted support contributed to quality of life (QOL) of CCSs in Japan.MethodsThe subjects were 46 CCSs of 16 years of age or older at the time of the survey, who had been diagnosed and treated for pediatric cancer. A self‐administered questionnaire survey was conducted to investigate the in‐hospital status during treatment, adjustment when returning to school, and administrative social support. The QOL of CCSs was also evaluated by the Medical Outcome Study 36‐Item Short‐Form Health Survey.ResultsTwenty‐four CCSs answered the questions. The respondents who had experienced school‐life problems tended to have lower role/social QOL scores (p = 0.046), whereas the CCSs who had experienced administrative counseling tended to have lower physical QOL scores (p = 0.036). The mental QOL scores tended to be higher in respondents who were informed of the exact diagnosis of cancer during hospitalization. The role/social QOL scores tended to be lower in respondents who advanced to their preferred career path.ConclusionsIt is essential for three stakeholders—health‐care providers, education offices, and public administrative agencies—to collaborate to share long‐term psychosocial issues or concerns related to employment or daily living that CCSs may encounter, and to establish a coordinated approach to support CCSs.
A Computational Conformal Geometry Approach to Calculate the Large Deformation of Plates/Shells With Arbitrary Shapes
Authors: Liu Yipeng , Fan Wei , Ren Hui 
Published: December 2023

Abstract
High-accuracy numerical methods to solve the nonlinear Föppl–von Kármán (FvK) equations usually work well only in simple domains such as rectangular regions. Computational conformal geometry (CCG) provides a systematic method to transform complicated surfaces into simple domains, preserving the orthogonal frames such that the corresponding FvK equations can be solved by more effective numerical methods. Based on CCG, we proposed a general method for solving large deformation and nonlinear vibration of plate/shell structures with arbitrary shapes. The method can map any complex surface conformal to a rectangular region, and then FvK equations are solved in the rectangular region to study nonlinear vibration problems of any arbitrary shape plates/shells. The conform map is calculated by solving Laplace equations on a fine Delauney triangular mesh on the surface, which is numerically robust, and the map is harmonic and subsequently C∞ smooth, such that all the evaluations and spatial derivatives required by high accuracy methods at the regular nodes can be accurately and efficiently calculated. A variational function that is equivalent to the FvK equations is provided, such that the FvK equations can be solved by multiple numerical methods. The degree-of-freedom in solving the FvK equations is usually much less than that in the finite element methods described by displacements. The effectiveness of the proposed approach is verified by several benchmark examples, and the current method is suitable for calculating the large deflections and nonlinear dynamical responses of plates/shallow shells with arbitrary shapes.
Early Prediction of Human Intention for Human–Robot Collaboration Using Transformer Network
Authors: Zhang Xinyao , Tian Sibo , Liang Xiao , Zheng Minghui , Behdad Sara 
Published: December 2023

Abstract
Human intention prediction plays a critical role in human–robot collaboration, as it helps robots improve efficiency and safety by accurately anticipating human intentions and proactively assisting with tasks. While current applications often focus on predicting intent once human action is completed, recognizing human intent in advance has received less attention. This study aims to equip robots with the capability to forecast human intent before completing an action, i.e., early intent prediction. To achieve this objective, we first extract features from human motion trajectories by analyzing changes in human joint distances. These features are then utilized in a Hidden Markov Model (HMM) to determine the state transition times from uncertain intent to certain intent. Second, we propose two models including a Transformer and a Bi-LSTM for classifying motion intentions. Then, we design a human–robot collaboration experiment in which the operator reaches multiple targets while the robot moves continuously following a predetermined path. The data collected through the experiment were divided into two groups: full-length data and partial data before state transitions detected by the HMM. Finally, the effectiveness of the suggested framework for predicting intentions is assessed using two different datasets, particularly in a scenario when motion trajectories are similar but underlying intentions vary. The results indicate that using partial data prior to the motion completion yields better accuracy compared to using full-length data. Specifically, the transformer model exhibits a 2% improvement in accuracy, while the Bi-LSTM model demonstrates a 6% increase in accuracy.
A Dynamical Model for the Control of a Guyed Tensegrity Beam Under Large Displacements
Authors: Kurka Paulo R. G. , Paiva Victor A. S. M. , Silva-Teixeira Luis H. , Ramos Paola G. , Izuka Jaime H. 
Published: December 2023

Abstract
Most studies regarding models of tensegrity systems miss the possibility of large static deformations or provide elaborate and lengthy solutions to determine the system dynamics. Contrarily, this work presents a straightforward methodology to find the dynamic characteristics of a guyed tensegrity beam structure, allowing the application of vibration control strategies in conditions of large deformations. The methodology is based on a low-order, adaptive, nonlinear finite element model with pre-stressed components. The method is applied to numerical and experimental models of a class 2 tensegrity structure with a high length-to-width aspect ratio. Image processing and accelerometer data are combined to extract the experimental natural frequencies of the structure, which are compared to numerical results. Prony’s method is applied to estimate damping, and a numerical control strategy is employed using the dynamical model of the structure.
Thinking Beyond the Default User: The Impact of Gender, Stereotypes, and Modality on Interpretation of User Needs
Authors: Schauer Anastasia M. , Schaufel Hunter , Nunn Margaret , Kohls Noah D. , Fu Katherine 
Published: December 2023

Abstract
Throughout the mechanical design process, designers, the majority of whom are men, often fail to consider the needs of women, resulting in consequences ranging from inconvenience to increased risk of serious injury or death. Although these biases are well studied in other fields of research, the mechanical design field lacks formal investigation into this phenomenon. In this study, engineering students (n = 301) took a survey in which they read a Persona describing a student makerspace user and a Walkthrough describing the user’s interaction with the makerspace while completing a project. During the Walkthrough, the user encountered various obstacles or Pain Points. Participants were asked to recall and evaluate the Pain Points that the user encountered and then evaluated their perceptions of the makerspace and user. The independent variables under investigation were the gender of the user Persona (woman, gender-neutral, or man), the Walkthrough room case (crafting or woodworking makerspace), and the modality of the Persona and Walkthrough (text- or audio-based). Results showed that participants from the Text-based modality were better able to recall Pain Points compared to participants from the Audio-based modality. Pain Points were assessed as more severe when they impacted women users, potentially stemming from protective paternalism. In addition to finding that the gender of a user impacted the way a task environment was perceived, results confirmed the presence of androcentrism, or “default man” assumptions, in the way designers view end users of unknown gender. Promisingly, providing user Persona information in an audio modality significantly reduced this bias compared to text-based modalities, indicating that providing richer detail in user personas has the capability to reduce gender bias in designers.
Lean Flame Stabilization With Nanosecond Plasma Discharges in a Gas Turbine Model Combustor
Authors: Blanchard Victorien P. , Roqué Frédéric , Scouflaire Philippe , Laux Christophe O , Ducruix Sébastien 
Published: December 2023

Abstract
This paper presents an experimental study of lean flames stabilization with nanosecond repetitively pulsed discharges. The two-stage, swirled-stabilized, multipoint injector BIMER operates at atmospheric pressure with methane-air mixtures in the present study. It is representative in its design of a realistic lean premixed prevaporized injector of gas turbine engines operated at a lab-scale level. The lean blow-off extension with plasma is characterized. The combustion efficiency and the pollutant emissions are quantified near blow-off with and without plasma for 50-kW flames. We show that it is possible to stabilize lean flames down to an equivalence ratio of 0.3, with less than 5 ppm of NOX emitted, thanks to nanosecond repetitively pulsed (NRP) discharges with an electric power that represents less than 0.25% of the flame thermal power. This study also clearly shows that it is necessary to account for the plasma system integration at the early stage of the combustor design to fully benefit from the plasma stabilizing effects on the flame.
Thermally generated spin current in the topological insulator Bi
2
Se
3
Authors: Jain Rakshit , Stanley Max , Bose Arnab , Richardella Anthony R. , Zhang Xiyue S. , Pillsbury Timothy , Muller David A. , Samarth Nitin , Ralph Daniel C. 
Published: December 2023

We present measurements of thermally generated transverse spin currents in the topological insulator Bi
2
Se
3
, thereby completing measurements of interconversions among the full triad of thermal gradients, charge currents, and spin currents. We accomplish this by comparing the spin Nernst magneto-thermopower to the spin Hall magnetoresistance for bilayers of Bi
2
Se
3
/CoFeB. We find that Bi
2
Se
3
does generate substantial thermally driven spin currents. A lower bound for the ratio of spin current density to thermal gradient is

J
s

∇

x

T

= (4.9 ± 0.9) × 10
6

(

ℏ

2
e

)

A

m

−
2

K

μ

m

−
1

, and a lower bound for the magnitude of the spin Nernst ratio is −0.61 ± 0.11. The spin Nernst ratio for Bi
2
Se
3
is the largest among all materials measured to date, two to three times larger compared to previous measurements for the heavy metals Pt and W. Strong thermally generated spin currents in Bi
2
Se
3
can be understood via Mott relations to be due to an overall large spin Hall conductivity and its dependence on electron energy.
The motility-matrix production switch in
Bacillus subtilis
—a modeling perspective
Authors: Dannenberg Simon , Penning Jonas , Simm Alexander , Klumpp Stefan 
Published: December 2023

ABSTRACT

Phenotype switching can be triggered by external stimuli and by intrinsic stochasticity. Here, we focus on the motility-matrix production switch in
Bacillus subtilis
. We use modeling to describe the SinR-SlrR bistable switch and its regulation by SinI and to distinguish different sources of stochasticity. Our simulations indicate that intrinsic fluctuations in the synthesis of SinI are insufficient to drive spontaneous switching and suggest that switching is triggered by upstream noise from the Spo0A phosphorelay.

IMPORTANCE

The switch from motility to matrix production is the first step toward biofilm formation and, thus, to multicellular behavior in
Bacillus subtilis
. The transition is governed by a bistable switch based on the interplay of the regulators SinR and SlrR, while SinI transmits upstream signals to that switch. Quantitative modeling can be used to study the switching dynamics. Here, we build such a model step by step to describe the dynamics of the switch and its regulation and to study how spontaneous switching is triggered by upstream noise from the Spo0A phosphorelay.
Lactate-lactylation-HSPA6 axis promotes PRRSV replication by impairing IFN-β production
Authors: Pang Yu , Zhou Yanrong , Wang Yucheng , Fang Liurong , Xiao Shaobo 
Published: December 2023

ABSTRACT

Lactate, traditionally considered a metabolic by-product, has recently been identified as a substrate for the induction of lactylation, a newly identified epigenetic modification that plays an important role in the regulation of host gene expression. Our previous study showed that lactate levels were significantly elevated in cells infected with the porcine reproductive and respiratory syndrome virus (PRRSV), an
Arterivirus
that has devastated the swine industry worldwide for over 30 years. However, the role of elevated lactate in PRRSV infections remains unknown. In this study, we found that lactate was required for optimal PRRSV proliferation, and PRRSV infection increased cellular lactylation in a dose-dependent manner. Using the Cleavage Under Targets and Tagmentation (CUT&Tag) combined with RNA sequencing (RNA-seq) to screen the downstream genes regulated by lactylation in PRRSV-infected cells, we found that PRRSV-induced lactylation activated the expression of heat shock 70 kDa protein 6 (HSPA6). Follow-up experiments showed that HSPA6 is important for PRRSV proliferation by negatively modulating interferon (IFN)-β induction. Mechanistically, HSPA6 impeded the interaction between TNF-receptor-associated factor 3 (TRAF3) and inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKKε), thereby hindering the production of IFN-β. Taken together, these results indicate that the activated lactate-lactylation-HSPA6 axis promotes viral growth by impairing IFN-β induction, providing new therapeutic targets for the prevention and control of PRRSV infection. The results presented here also link lactylation to the virus life cycle, improving our understanding of epigenetic regulation in viral infection.

IMPORTANCE
As a newly identified epigenetic modification, lactate-induced lactylation has received attentions because it plays important roles in gene expression and contributes to tumorigenesis and the innate immune response. Previous studies showed that many viruses upregulate cellular lactate levels; however, whether virus-elevated lactate induces lactylation and the subsequent biological significance of the modification to viral infection have not been reported. In this study, we demonstrated that porcine reproductive and respiratory syndrome virus (PRRSV) infection induced cellular lactylation, which, in turn, upregulated the expression of HSPA6, an IFN-negative regulator. We also dissected the mechanism by which HSPA6 negatively regulates IFN-β production. To our knowledge, this is the first report to study virus-induced lactylation and establish the relationship between lactylation and virus infection.
Draft genome sequencing of a multidrug-resistant
Salmonella enterica
subspecies enterica serovar Typhimurium strain isolated from chicken in Bangladesh
Authors: Popy Najmun Nahar , Hoque M. Nazmul , Khan Mohammad Ferdousur Rahman , Biswas Limon , Rahman Mohammad Habibur , Saiduzzaman Md. , Rahman Marzia , Rahman Md. Bahanur 
Published: December 2023

ABSTRACT

Herein this study, we sequenced the genome of a multidrug-resistant
Salmonella enterica
serovar Typhimurium strain MBR-MFRK-23 isolated from the liver tissue of a diseased layer chicken. The 4,964,854-bp draft genome comprises 50 contigs with 50.5× coverage and 52.1% GC content and is typed as
S. enterica
sequence type 19.